SMTL ID : 4v8k.2 (1 other biounit)

Crystal structure of the LH1-RC complex from Thermochromatium tepidum in P21 form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-1-1-1-1-16-16-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 21 residues within 4Å: Chain A: Y.76, Q.77, N.78, V.79, Q.80, V.81, L.82, F.90, M.94, V.97, T.98, G.106, C.107, C.110, H.111, W.116, A.117, K.124, S.127, R.128 Ligands: HEM.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Y.76, A:Y.76, A:V.79, A:F.90, A:V.97, A:W.116, A:W.116, A:K.124 Hydrogen bonds: A:N.78, A:Q.80, A:V.81, A:L.82 Salt bridges: A:R.128 pi-Stacking: A:F.90, A:H.111, A:H.111 Metal complexes: A:H.111 HEM.2: 27 residues within 4Å: Chain A: V.97, V.101, Y.109, Y.122, T.123, V.126, S.127, M.130, L.133, V.134, V.150, T.151, C.152, C.155, H.156, P.160, V.161, P.162, I.279, I.284, L.291, R.295, L.303, R.304, V.305 Ligands: HEM.1, HEM.4 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:V.97, A:V.101, A:V.126, A:M.130, A:L.133, A:V.134, A:V.150, A:V.161, A:P.162, A:I.279, A:I.284, A:V.305 Salt bridges: A:R.295, A:R.295 pi-Stacking: A:H.156 pi-Cation interactions: A:H.156 Metal complexes: A:H.156 HEM.3: 21 residues within 4Å: Chain A: I.210, R.211, I.212, T.213, T.232, M.236, L.243, V.245, G.246, C.247, C.250, H.251, F.256, N.257, W.259, R.266, A.269, W.270, R.274 Chain C: I.191, Y.317 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:T.232, A:L.243, A:F.256, A:F.256, A:W.259, A:R.266, A:A.269, C:I.191 Hydrogen bonds: A:I.212, A:T.213, A:T.213, A:W.270, C:Y.317 Salt bridges: A:R.274 pi-Stacking: A:H.251, A:H.251, A:H.251, A:F.256 pi-Cation interactions: A:R.266 Metal complexes: A:H.251 HEM.4: 21 residues within 4Å: Chain A: H.144, V.145, A.146, T.148, G.149, V.150, L.204, K.265, T.268, A.269, A.272, I.273, V.276, V.305, S.306, C.307, C.310, H.311, N.315, K.316 Ligands: HEM.2 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:A.146, A:V.150, A:L.204, A:T.268, A:A.272, A:V.276, A:V.305, A:K.316 Hydrogen bonds: A:T.148, A:T.148 Salt bridges: A:K.265, A:K.316 pi-Stacking: A:H.144, A:H.144, A:H.311, A:H.311, A:H.311 pi-Cation interactions: A:H.144 Metal complexes: A:H.144, A:H.311

17 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: Q.183, N.184, E.230 Chain C: E.96 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:E.230, C:E.96, C:E.96, H2O.1 CA.20: 6 residues within 4Å: Chain 9: L.47 Chain E: W.46, D.49, N.50, I.51 Chain F: R.44 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain 9 Metal complexes: E:W.46, E:D.49, 9:L.47 CA.23: 7 residues within 4Å: Chain F: L.47 Chain G: W.46, L.47, D.49, N.50, I.51 Chain H: R.44 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain F Metal complexes: G:W.46, G:D.49, G:I.51, F:L.47 CA.26: 7 residues within 4Å: Chain H: L.47 Chain I: N.45, W.46, L.47, D.49, N.50, I.51 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain H Metal complexes: I:W.46, I:D.49, H:L.47 CA.31: 7 residues within 4Å: Chain J: L.47 Chain K: W.46, D.49, N.50, I.51 Chain L: Y.43, R.44 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain K Metal complexes: J:L.47, K:W.46, K:D.49, K:I.51 CA.34: 6 residues within 4Å: Chain L: L.47 Chain M: W.46, D.49, N.50, I.51 Chain N: R.44 5 PLIP interactions: 4 interactions with chain M, 1 interactions with chain L Metal complexes: M:W.46, M:D.49, M:N.50, M:I.51, L:L.47 CA.38: 9 residues within 4Å: Chain N: L.47 Chain O: N.45, W.46, L.47, D.48, D.49, N.50, I.51 Chain P: R.44 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:W.46, O:D.49, O:I.51 CA.44: 7 residues within 4Å: Chain P: L.47 Chain Q: N.45, W.46, D.49, N.50, I.51 Chain R: R.44 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain P Metal complexes: Q:W.46, Q:D.49, Q:I.51, P:L.47 CA.47: 6 residues within 4Å: Chain R: L.47 Chain S: N.45, W.46, D.49, N.50, I.51 4 PLIP interactions: 3 interactions with chain S, 1 interactions with chain R Metal complexes: S:W.46, S:D.49, S:I.51, R:L.47 CA.51: 5 residues within 4Å: Chain T: L.47 Chain U: W.46, D.49, N.50, I.51 4 PLIP interactions: 3 interactions with chain U, 1 interactions with chain T Metal complexes: U:W.46, U:D.49, U:I.51, T:L.47 CA.56: 5 residues within 4Å: Chain V: L.47 Chain W: W.46, D.49, N.50, I.51 5 PLIP interactions: 4 interactions with chain W, 1 interactions with chain V Metal complexes: W:W.46, W:D.49, W:N.50, W:I.51, V:L.47 CA.60: 6 residues within 4Å: Chain X: L.47 Chain Y: W.46, D.49, N.50, I.51 Chain Z: R.44 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain X Metal complexes: Y:W.46, Y:D.49, Y:I.51, X:L.47 CA.63: 5 residues within 4Å: Chain 0: W.46, D.49, N.50, I.51 Chain Z: L.47 4 PLIP interactions: 1 interactions with chain Z, 3 interactions with chain 0 Metal complexes: Z:L.47, 0:W.46, 0:D.49, 0:I.51 CA.68: 6 residues within 4Å: Chain 1: L.47 Chain 2: W.46, D.49, N.50, I.51 Chain 3: R.44 3 PLIP interactions: 2 interactions with chain 2, 1 interactions with chain 1 Metal complexes: 2:W.46, 2:D.49, 1:L.47 CA.71: 6 residues within 4Å: Chain 3: L.47 Chain 4: W.46, D.49, N.50, I.51, P.52 4 PLIP interactions: 1 interactions with chain 3, 3 interactions with chain 4 Metal complexes: 3:L.47, 4:W.46, 4:D.49, 4:I.51 CA.75: 6 residues within 4Å: Chain 5: W.46, L.47 Chain 6: W.46, L.47, D.49, N.50 3 PLIP interactions: 2 interactions with chain 6, 1 interactions with chain 5 Metal complexes: 6:W.46, 6:D.49, 5:L.47 CA.79: 5 residues within 4Å: Chain 7: L.47 Chain 8: W.46, D.49, N.50, I.51 3 PLIP interactions: 1 interactions with chain 7, 2 interactions with chain 8 Metal complexes: 7:L.47, 8:W.46, 8:D.49

36 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)(Covalent)

BCL.6: 24 residues within 4Å: Chain B: F.106, A.133, Y.137, L.140, V.166, S.167, G.170, H.177, H.182, A.185, I.186, F.189, S.253, A.254, C.256, I.257 Chain C: T.186, Y.197, Y.210 Ligands: BPH.7, BCL.9, BCL.10, BCL.11, MQ8.14 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.106, B:F.106, B:A.133, B:Y.137, B:L.140, B:V.166, B:V.166, B:A.185, B:I.186, B:F.189, B:F.189, B:I.257 Metal complexes: B:H.182 Hydrogen bonds: C:T.186 BCL.9: 19 residues within 4Å: Chain B: V.47, I.50, Y.137, L.140, F.155, I.159, L.160, H.162, L.163 Chain C: M.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.6, BPH.7, BCL.11, MQ8.14 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain B, Hydrophobic interactions: C:I.206, C:I.206, C:A.207, C:L.214, B:V.47, B:I.50, B:Y.137, B:L.140, B:F.155 pi-Stacking: C:Y.210 Metal complexes: B:H.162 BCL.10: 17 residues within 4Å: Chain B: H.182, M.183, I.186, S.187, F.190, T.191 Chain C: F.156, L.160, V.175, I.179, H.182, L.183 Ligands: BCL.6, BCL.11, BPH.12, CRT.15, PEF.43 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:F.156, C:L.160, C:V.175, C:I.179, B:I.186, B:I.186 Metal complexes: C:H.182 Hydrogen bonds: B:T.191 pi-Stacking: B:F.190 BCL.11: 34 residues within 4Å: Chain B: Y.171, H.177, F.190 Chain C: I.68, I.71, L.122, I.126, A.153, I.154, F.156, Y.157, L.160, F.177, W.185, T.186, A.187, F.189, S.190, L.196, Y.197, H.202, S.205, I.206, L.209, Y.210, A.280, G.283, I.284 Ligands: BCL.6, BCL.9, BCL.10, BPH.12, CRT.15, PEF.43 24 PLIP interactions: 22 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:I.68, C:I.71, C:L.122, C:I.126, C:I.126, C:I.126, C:I.154, C:F.156, C:Y.157, C:Y.157, C:F.177, C:W.185, C:A.187, C:F.189, C:L.196, C:Y.197, C:I.206, C:L.209, C:I.284, C:I.284, B:F.190 Salt bridges: C:H.202 Metal complexes: C:H.202 pi-Cation interactions: B:H.177 BCL.18: 16 residues within 4Å: Chain 8: L.15, I.24 Chain E: V.25, Q.28, I.29, G.32, H.36, W.46 Chain F: W.29, L.32, V.33, A.36, H.37 Ligands: BCL.21, CRT.81, BCL.82 13 PLIP interactions: 4 interactions with chain F, 2 interactions with chain 8, 7 interactions with chain E, Hydrophobic interactions: F:W.29, F:W.29, F:A.36, 8:L.15, 8:I.24, E:V.25, E:Q.28, E:I.29, E:W.46, E:W.46, E:W.46 Hydrogen bonds: F:H.37 Metal complexes: E:H.36 BCL.21: 17 residues within 4Å: Chain E: Q.28, L.31, G.32, I.35, H.36, V.39, D.43 Chain F: W.29, F.30, V.33, H.37, L.38, W.46 Chain G: L.47 Ligands: BCL.18, CRT.22, BCL.24 15 PLIP interactions: 9 interactions with chain F, 5 interactions with chain E, 1 interactions with chain G, Hydrophobic interactions: F:F.30, F:F.30, F:V.33, F:V.33, F:H.37, F:W.46, F:W.46, F:W.46, E:L.31, E:I.35, E:V.39, G:L.47 Metal complexes: F:H.37 Hydrogen bonds: E:Q.28 pi-Stacking: E:H.36 BCL.24: 19 residues within 4Å: Chain E: W.12, I.35 Chain G: V.25, Q.28, I.29, G.32, H.36, V.39, W.46, L.47 Chain H: W.29, L.32, V.33, A.36, H.37 Ligands: CRT.19, BCL.21, CRT.22, BCL.25 12 PLIP interactions: 6 interactions with chain G, 4 interactions with chain H, 2 interactions with chain E, Hydrophobic interactions: G:Q.28, G:I.29, G:V.39, G:W.46, G:W.46, H:W.29, H:W.29, H:W.29, H:A.36, E:W.12, E:I.35 Metal complexes: G:H.36 BCL.25: 15 residues within 4Å: Chain G: Q.28, L.31, G.32, I.35, H.36 Chain H: W.29, F.30, V.33, V.34, H.37, L.38, W.46 Ligands: CRT.19, BCL.24, BCL.27 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain G, Hydrophobic interactions: H:F.30, H:F.30, H:V.33, H:V.34, H:H.37, H:L.38, H:W.46, H:W.46, H:W.46, G:I.35 Metal complexes: H:H.37 BCL.27: 21 residues within 4Å: Chain G: W.12, V.20, I.24 Chain H: F.22 Chain I: L.21, V.25, Q.28, I.29, G.32, H.36, L.44, W.46 Chain J: W.29, V.33, A.36, H.37, A.40 Ligands: CRT.19, BCL.25, BCL.29, CRT.30 17 PLIP interactions: 6 interactions with chain J, 8 interactions with chain I, 2 interactions with chain G, 1 interactions with chain H, Hydrophobic interactions: J:W.29, J:W.29, J:W.29, J:W.29, J:A.36, J:A.40, I:L.21, I:Q.28, I:I.29, I:L.44, I:W.46, I:W.46, I:W.46, G:V.20, G:I.24, H:F.22 Metal complexes: I:H.36 BCL.29: 17 residues within 4Å: Chain I: Q.28, L.31, G.32, I.35, H.36 Chain J: W.29, F.30, V.33, H.37, W.46 Chain K: L.47 Chain L: L.32, I.35, L.39 Ligands: BCL.27, CRT.30, BCL.32 13 PLIP interactions: 7 interactions with chain J, 1 interactions with chain I, 4 interactions with chain L, 1 interactions with chain K, Hydrophobic interactions: J:F.30, J:V.33, J:W.46, J:W.46, J:W.46, J:W.46, I:I.35, L:L.32, L:I.35, L:L.39, L:L.39, K:L.47 Metal complexes: J:H.37 BCL.32: 18 residues within 4Å: Chain J: F.22, M.26 Chain K: Q.28, I.29, G.32, H.36, V.39, W.46, L.47 Chain L: W.29, L.32, V.33, A.36, H.37 Ligands: CRT.28, BCL.29, CRT.30, BCL.33 11 PLIP interactions: 6 interactions with chain K, 4 interactions with chain L, 1 interactions with chain J, Hydrophobic interactions: K:Q.28, K:V.39, K:W.46, K:W.46, K:W.46, L:W.29, L:W.29, L:W.29, L:A.36, J:F.22 Metal complexes: K:H.36 BCL.33: 17 residues within 4Å: Chain K: Q.28, L.31, G.32, I.35, H.36, V.39, D.43 Chain L: W.29, F.30, V.33, V.34, H.37, L.38, W.41, W.46 Ligands: BCL.32, BCL.35 12 PLIP interactions: 3 interactions with chain K, 9 interactions with chain L, Hydrophobic interactions: K:L.31, K:I.35, K:V.39, L:F.30, L:V.33, L:V.34, L:H.37, L:L.38, L:W.41, L:W.46, L:W.46 Metal complexes: L:H.37 BCL.35: 18 residues within 4Å: Chain K: I.11 Chain L: F.22 Chain M: V.25, Q.28, I.29, G.32, H.36, V.39, W.46, L.47 Chain N: W.29, L.32, A.36, H.37 Ligands: CRT.28, BCL.33, BCL.36, CRT.37 14 PLIP interactions: 7 interactions with chain M, 1 interactions with chain L, 2 interactions with chain K, 4 interactions with chain N, Hydrophobic interactions: M:Q.28, M:V.39, M:W.46, M:W.46, M:W.46, M:W.46, L:F.22, K:I.11, K:I.11, N:W.29, N:W.29, N:W.29, N:A.36 Metal complexes: M:H.36 BCL.36: 18 residues within 4Å: Chain M: Q.28, L.31, G.32, I.35, H.36 Chain N: W.29, F.30, V.33, H.37, W.46, L.47 Chain O: L.47 Chain P: L.39, A.40, Y.43 Ligands: BCL.35, CRT.37, BCL.39 9 PLIP interactions: 1 interactions with chain P, 1 interactions with chain M, 6 interactions with chain N, 1 interactions with chain O, Hydrophobic interactions: P:A.40, M:I.35, N:F.30, N:V.33, N:W.46, N:W.46, N:L.47, O:L.47 Metal complexes: N:H.37 BCL.39: 19 residues within 4Å: Chain M: W.12 Chain N: F.22, M.26 Chain O: V.25, Q.28, I.29, G.32, H.36, W.46, L.47 Chain P: W.29, L.32, V.33, A.36, H.37 Ligands: BCL.36, CRT.37, BCL.41, CRT.42 15 PLIP interactions: 8 interactions with chain O, 1 interactions with chain M, 5 interactions with chain P, 1 interactions with chain N, Hydrophobic interactions: O:V.25, O:Q.28, O:I.29, O:W.46, O:W.46, O:W.46, O:W.46, M:W.12, P:W.29, P:W.29, P:W.29, P:A.36, N:F.22 Metal complexes: O:H.36 Hydrogen bonds: P:H.37 BCL.41: 14 residues within 4Å: Chain O: Q.28, L.31, G.32, I.35, H.36 Chain P: W.29, F.30, V.33, H.37, W.46 Chain Q: L.47 Ligands: BCL.39, CRT.42, BCL.45 10 PLIP interactions: 2 interactions with chain O, 1 interactions with chain Q, 7 interactions with chain P, Hydrophobic interactions: O:I.35, Q:L.47, P:F.30, P:F.30, P:V.33, P:W.46, P:W.46, P:W.46 Hydrogen bonds: O:Q.28 Metal complexes: P:H.37 BCL.45: 16 residues within 4Å: Chain O: F.27 Chain P: F.22 Chain Q: Q.28, I.29, H.36, W.46, L.47 Chain R: W.29, L.32, V.33, A.36, H.37 Ligands: CRT.40, BCL.41, CRT.42, BCL.46 11 PLIP interactions: 5 interactions with chain Q, 4 interactions with chain R, 1 interactions with chain O, 1 interactions with chain P, Hydrophobic interactions: Q:Q.28, Q:I.29, Q:W.46, Q:W.46, R:W.29, R:W.29, R:W.29, R:A.36, O:F.27, P:F.22 Metal complexes: Q:H.36 BCL.46: 14 residues within 4Å: Chain Q: Q.28, L.31, G.32, I.35, H.36 Chain R: W.29, F.30, V.33, H.37, W.41, W.46 Ligands: CRT.40, BCL.45, BCL.48 9 PLIP interactions: 8 interactions with chain R, 1 interactions with chain Q, Hydrophobic interactions: R:F.30, R:V.33, R:W.41, R:W.46, R:W.46, R:W.46, R:W.46, Q:I.35 Metal complexes: R:H.37 BCL.48: 17 residues within 4Å: Chain Q: I.24, I.35, V.39 Chain S: L.21, V.25, Q.28, I.29, H.36, W.46 Chain T: W.29, L.32, V.33, A.36, H.37 Ligands: CRT.40, BCL.46, BCL.50 11 PLIP interactions: 7 interactions with chain S, 1 interactions with chain T, 3 interactions with chain Q, Hydrophobic interactions: S:L.21, S:Q.28, S:I.29, S:W.46, S:W.46, T:W.29, Q:I.24, Q:I.35, Q:V.39 pi-Stacking: S:W.46 Metal complexes: S:H.36 BCL.50: 18 residues within 4Å: Chain S: Q.28, L.31, G.32, I.35, H.36, L.44 Chain T: W.29, F.30, V.33, H.37, W.46 Chain U: L.47 Chain V: L.39, A.40, Y.43 Ligands: BCL.48, CRT.49, BCL.52 9 PLIP interactions: 1 interactions with chain S, 4 interactions with chain T, 3 interactions with chain V, 1 interactions with chain U, Hydrophobic interactions: S:L.44, T:F.30, T:V.33, T:W.46, V:L.39, V:L.39, V:Y.43, U:L.47 Metal complexes: T:H.37 BCL.52: 18 residues within 4Å: Chain S: S.23, I.24, I.35 Chain U: V.25, Q.28, I.29, G.32, H.36, W.46 Chain V: W.29, L.32, V.33, A.36, H.37, A.40 Ligands: CRT.49, BCL.50, BCL.54 14 PLIP interactions: 3 interactions with chain S, 8 interactions with chain U, 3 interactions with chain V, Hydrophobic interactions: S:I.24, S:I.35, S:I.35, U:V.25, U:Q.28, U:I.29, U:W.46, U:W.46, U:W.46, U:W.46, V:W.29, V:W.29, V:A.40 Metal complexes: U:H.36 BCL.54: 13 residues within 4Å: Chain U: Q.28, L.31, G.32, I.35, H.36 Chain V: W.29, F.30, H.37, W.41, W.46 Ligands: BCL.52, CRT.55, BCL.57 8 PLIP interactions: 7 interactions with chain V, 1 interactions with chain U, Hydrophobic interactions: V:F.30, V:W.41, V:W.41, V:W.46, V:W.46, V:W.46, U:I.35 Metal complexes: V:H.37 BCL.57: 20 residues within 4Å: Chain U: L.15, V.20, I.35 Chain V: F.22, M.26 Chain W: L.21, V.25, Q.28, I.29, H.36, W.46 Chain X: W.29, L.32, V.33, A.36, H.37 Ligands: CRT.53, BCL.54, CRT.55, BCL.59 14 PLIP interactions: 6 interactions with chain W, 4 interactions with chain X, 3 interactions with chain U, 1 interactions with chain V, Hydrophobic interactions: W:L.21, W:Q.28, W:I.29, W:W.46, W:W.46, X:W.29, X:W.29, X:W.29, X:A.36, U:L.15, U:V.20, U:I.35, V:F.22 Metal complexes: W:H.36 BCL.59: 15 residues within 4Å: Chain W: Q.28, L.31, G.32, I.35, H.36 Chain X: W.29, F.30, V.33, H.37, W.46 Chain Y: L.47 Chain Z: L.39 Ligands: CRT.53, BCL.57, BCL.61 11 PLIP interactions: 2 interactions with chain W, 1 interactions with chain Y, 7 interactions with chain X, 1 interactions with chain Z, Hydrophobic interactions: W:L.31, W:I.35, Y:L.47, X:F.30, X:V.33, X:W.46, X:W.46, X:W.46, X:W.46, Z:L.39 Metal complexes: X:H.37 BCL.61: 20 residues within 4Å: Chain W: I.11, L.15, I.24 Chain Y: V.25, Q.28, I.29, G.32, L.33, H.36, W.46 Chain Z: W.29, L.32, V.33, A.36, H.37, A.40 Ligands: CRT.53, CRT.58, BCL.59, BCL.62 10 PLIP interactions: 4 interactions with chain Y, 3 interactions with chain W, 3 interactions with chain Z, Hydrophobic interactions: Y:Q.28, Y:I.29, Y:W.46, W:I.11, W:L.15, W:I.24, Z:W.29, Z:A.36, Z:A.40 Metal complexes: Y:H.36 BCL.62: 17 residues within 4Å: Chain 0: L.47 Chain 1: L.32, L.39 Chain Y: Q.28, L.31, G.32, I.35, H.36, V.39 Chain Z: W.29, F.30, V.33, H.37, W.41, W.46 Ligands: BCL.61, BCL.64 11 PLIP interactions: 7 interactions with chain Z, 2 interactions with chain Y, 1 interactions with chain 0, 1 interactions with chain 1, Hydrophobic interactions: Z:F.30, Z:V.33, Z:W.41, Z:W.46, Z:W.46, Z:W.46, Y:L.31, 0:L.47, 1:L.39 Metal complexes: Z:H.37 Hydrogen bonds: Y:Q.28 BCL.64: 21 residues within 4Å: Chain 0: L.21, V.25, Q.28, I.29, G.32, H.36, V.39, W.46 Chain 1: W.29, L.32, V.33, A.36, H.37 Chain Y: I.11, W.12, L.15, V.20 Ligands: CRT.58, BCL.62, BCL.66, CRT.67 15 PLIP interactions: 3 interactions with chain 1, 7 interactions with chain 0, 5 interactions with chain Y, Hydrophobic interactions: 1:W.29, 1:A.36, 0:L.21, 0:Q.28, 0:I.29, 0:V.39, 0:W.46, Y:I.11, Y:I.11, Y:W.12, Y:L.15, Y:V.20 Hydrogen bonds: 1:H.37, 0:L.33 Metal complexes: 0:H.36 BCL.66: 14 residues within 4Å: Chain 0: Q.28, L.31, G.32, I.35, H.36 Chain 1: W.29, F.30, V.33, H.37, W.41, W.46 Ligands: BCL.64, CRT.67, BCL.69 8 PLIP interactions: 8 interactions with chain 1, Hydrophobic interactions: 1:F.30, 1:V.33, 1:W.46, 1:W.46, 1:W.46, 1:W.46 pi-Stacking: 1:H.37 Metal complexes: 1:H.37 BCL.69: 21 residues within 4Å: Chain 0: I.11, W.12, V.20 Chain 1: F.22, M.26 Chain 2: V.25, Q.28, I.29, G.32, H.36, L.44, W.46 Chain 3: W.29, L.32, V.33, A.36, H.37 Ligands: CRT.65, BCL.66, CRT.67, BCL.70 15 PLIP interactions: 8 interactions with chain 2, 1 interactions with chain 1, 2 interactions with chain 0, 4 interactions with chain 3, Hydrophobic interactions: 2:Q.28, 2:Q.28, 2:I.29, 2:L.44, 2:W.46, 2:W.46, 2:W.46, 1:F.22, 0:I.11, 0:V.20, 3:W.29, 3:W.29, 3:W.29, 3:A.36 Metal complexes: 2:H.36 BCL.70: 15 residues within 4Å: Chain 2: Q.28, L.31, G.32, I.35, H.36, L.44 Chain 3: W.29, F.30, V.33, H.37, W.46 Chain 5: Y.43 Ligands: CRT.65, BCL.69, BCL.72 12 PLIP interactions: 7 interactions with chain 3, 5 interactions with chain 2, Hydrophobic interactions: 3:F.30, 3:F.30, 3:F.30, 3:V.33, 3:W.46, 3:W.46, 2:L.31, 2:I.35, 2:L.44 Metal complexes: 3:H.37 Hydrogen bonds: 2:Q.28 pi-Stacking: 2:H.36 BCL.72: 20 residues within 4Å: Chain 2: I.11, W.12, L.15 Chain 3: F.22 Chain 4: Q.28, I.29, G.32, L.33, H.36, V.39, W.46 Chain 5: W.29, L.32, V.33, A.36, H.37 Ligands: CRT.65, BCL.70, BCL.74, CRT.76 15 PLIP interactions: 3 interactions with chain 2, 7 interactions with chain 4, 4 interactions with chain 5, 1 interactions with chain 3, Hydrophobic interactions: 2:I.11, 2:W.12, 2:L.15, 4:Q.28, 4:I.29, 4:V.39, 4:W.46, 4:W.46, 4:W.46, 5:W.29, 5:W.29, 5:W.29, 5:A.36, 3:F.22 Metal complexes: 4:H.36 BCL.74: 17 residues within 4Å: Chain 4: Q.28, L.31, G.32, I.35, H.36, V.39, L.44 Chain 5: W.29, F.30, V.33, H.37, W.46 Chain 6: L.47 Chain 7: L.39 Ligands: BCL.72, CRT.76, BCL.77 7 PLIP interactions: 3 interactions with chain 5, 1 interactions with chain 6, 2 interactions with chain 4, 1 interactions with chain 7, Hydrophobic interactions: 5:F.30, 5:V.33, 6:L.47, 4:I.35, 4:L.44, 7:L.39 Metal complexes: 5:H.37 BCL.77: 18 residues within 4Å: Chain 4: V.20 Chain 6: L.21, V.22, V.25, Q.28, I.29, G.32, H.36, V.39, W.46 Chain 7: W.29, V.33, A.36, H.37 Ligands: CRT.73, BCL.74, CRT.76, BCL.78 18 PLIP interactions: 12 interactions with chain 6, 5 interactions with chain 7, 1 interactions with chain 4, Hydrophobic interactions: 6:L.21, 6:V.22, 6:V.25, 6:V.25, 6:Q.28, 6:I.29, 6:V.39, 6:W.46, 6:W.46, 6:W.46, 7:W.29, 7:W.29, 7:W.29, 7:W.29, 7:A.36, 4:V.20 Hydrogen bonds: 6:G.32 Metal complexes: 6:H.36 BCL.78: 15 residues within 4Å: Chain 6: Q.28, L.31, G.32, I.35, H.36 Chain 7: W.29, F.30, V.33, V.34, H.37, W.41, W.46 Ligands: CRT.73, BCL.77, BCL.80 13 PLIP interactions: 3 interactions with chain 6, 10 interactions with chain 7, Hydrophobic interactions: 6:I.35, 6:I.35, 7:F.30, 7:F.30, 7:V.33, 7:V.34, 7:W.41, 7:W.46, 7:W.46, 7:W.46, 7:W.46 Hydrogen bonds: 6:Q.28 Metal complexes: 7:H.37 BCL.80: 18 residues within 4Å: Chain 6: L.15, V.20, V.39 Chain 7: F.22 Chain 8: V.25, Q.28, I.29, G.32, H.36, W.46 Chain 9: W.29, L.32, V.33, A.36, H.37 Ligands: CRT.73, BCL.78, BCL.82 12 PLIP interactions: 3 interactions with chain 6, 4 interactions with chain 8, 4 interactions with chain 9, 1 interactions with chain 7, Hydrophobic interactions: 6:L.15, 6:V.20, 6:V.39, 8:Q.28, 8:I.29, 8:W.46, 9:W.29, 9:W.29, 9:W.29, 9:W.29, 7:F.22 Metal complexes: 8:H.36 BCL.82: 16 residues within 4Å: Chain 8: Q.28, L.31, G.32, I.35, H.36 Chain 9: W.29, F.30, V.33, V.34, H.37, L.38, W.41, W.46 Ligands: BCL.18, BCL.80, CRT.81 15 PLIP interactions: 13 interactions with chain 9, 2 interactions with chain 8, Hydrophobic interactions: 9:F.30, 9:V.33, 9:V.33, 9:V.34, 9:H.37, 9:L.38, 9:W.41, 9:W.46, 9:W.46, 9:W.46, 9:W.46, 9:W.46, 8:I.35 Metal complexes: 9:H.37 Hydrogen bonds: 8:Q.28

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.7: 30 residues within 4Å: Chain B: F.42, T.43, G.46, V.47, A.102, A.105, F.106, W.109, E.113, V.126, A.129, F.130, A.133, Y.137, Y.157, G.158, I.159, H.162, F.189, A.246, L.247, A.250 Chain C: Y.210, A.213, L.214, W.252, T.255, M.256 Ligands: BCL.6, BCL.9 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.43, B:V.47, B:A.102, B:A.105, B:F.106, B:A.129, B:F.130, B:F.130, B:A.133, B:Y.137, B:Y.157, B:Y.157, B:H.162, B:F.189, B:A.246, B:L.247, B:A.250, C:A.213 pi-Stacking: B:F.130 BPH.12: 24 residues within 4Å: Chain B: F.190, C.193, L.194, S.197, I.228, V.229 Chain C: I.61, G.64, L.65, I.68, S.125, I.126, W.129, L.146, A.149, F.150, A.153, A.273, T.276, V.277 Ligands: BCL.10, BCL.11, CRT.15, PEF.43 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.61, C:L.65, C:L.65, C:I.68, C:A.149, C:F.150, C:F.150, C:T.276, C:V.277 pi-Stacking: C:F.150

1 x UQ8: Ubiquinone-8(Non-covalent)

UQ8.8: 23 residues within 4Å: Chain A: M.19 Chain B: F.188, T.191, M.198, H.199, L.202, E.221, N.222, F.225, Y.231, S.232, I.233, G.234, A.235, I.238, L.241, L.243, F.244, S.248, F.251, W.252 Chain C: I.7 Ligands: PEF.43 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.188, B:F.188, B:T.191, B:M.198, B:F.225, B:F.225, B:F.225, B:F.225, B:Y.231, B:I.233, B:I.238, B:L.241, B:L.243, B:F.244, B:F.244, B:F.251, B:W.252, C:I.7 Hydrogen bonds: B:I.233, B:G.234

1 x FE: FE (III) ION(Non-covalent)

FE.13: 5 residues within 4Å: Chain B: H.199, H.239 Chain C: H.219, E.234, H.266 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.219, C:E.234, C:H.266, B:H.199, B:H.239

1 x MQ8: MENAQUINONE 8(Non-covalent)

MQ8.14: 18 residues within 4Å: Chain B: T.43, V.47, W.109 Chain C: L.215, H.219, T.222, A.248, A.249, W.252, M.256, F.258, N.259, V.260, T.261, M.262, I.265 Ligands: BCL.6, BCL.9 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.215, C:A.248, C:A.249, C:W.252, C:W.252, C:F.258, C:F.258, C:V.260, C:I.265, C:I.265, C:I.265, B:T.43, B:V.47, B:W.109 Hydrogen bonds: C:V.260 pi-Stacking: C:W.252

17 x CRT: SPIRILLOXANTHIN(Non-covalent)

CRT.15: 21 residues within 4Å: Chain C: G.72, F.73, L.76, L.116, G.119, L.120, T.123, Y.157, L.160, G.161, F.162, V.175, P.176, F.177, G.178, I.179, H.182 Chain Q: M.37 Ligands: BCL.10, BCL.11, BPH.12 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.116, C:L.120, C:L.120, C:F.162, C:F.162, C:V.175, C:F.177, C:F.177, C:F.177, C:H.182 CRT.19: 20 residues within 4Å: Chain E: L.8, K.10, I.11, L.13 Chain G: L.21, I.24, F.27, L.31, I.35, I.38 Chain H: E.17, F.18, I.21, F.22, M.26 Chain I: L.33, H.36 Ligands: BCL.24, BCL.25, BCL.27 15 PLIP interactions: 5 interactions with chain H, 6 interactions with chain G, 2 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: H:E.17, H:F.18, H:I.21, H:F.22, H:F.22, G:L.21, G:I.24, G:F.27, G:L.31, G:L.31, G:I.38, I:L.33, I:L.33, E:I.11, E:I.11 CRT.22: 20 residues within 4Å: Chain 8: L.8, K.10, I.11 Chain E: I.24, F.27, Q.28, L.31, I.35 Chain F: E.17, F.18, I.21, F.22, S.25, W.29 Chain G: G.32, L.33, H.36, M.37 Ligands: BCL.21, BCL.24 16 PLIP interactions: 2 interactions with chain G, 8 interactions with chain F, 3 interactions with chain 8, 3 interactions with chain E Hydrophobic interactions: G:L.33, G:H.36, F:F.18, F:F.18, F:F.18, F:I.21, F:F.22, F:F.22, F:F.22, F:W.29, 8:L.8, 8:K.10, 8:I.11, E:I.24, E:F.27, E:L.31 CRT.28: 20 residues within 4Å: Chain I: L.8, K.10, I.11, L.13 Chain K: I.24, F.27, Q.28, L.31, I.38 Chain L: E.17, F.18, I.21, F.22, S.25 Chain M: G.32, L.33, H.36, M.37 Ligands: BCL.32, BCL.35 12 PLIP interactions: 2 interactions with chain I, 4 interactions with chain K, 1 interactions with chain M, 5 interactions with chain L Hydrophobic interactions: I:I.11, I:I.11, K:I.24, K:F.27, K:F.27, K:I.38, M:H.36, L:F.18, L:F.18, L:I.21, L:I.21, L:F.22 CRT.30: 21 residues within 4Å: Chain G: K.10, I.11, L.13 Chain I: I.24, F.27, Q.28, L.31, I.35, I.38 Chain J: E.17, F.18, I.21, F.22, S.25, M.26 Chain K: L.33, H.36, M.37 Ligands: BCL.27, BCL.29, BCL.32 13 PLIP interactions: 5 interactions with chain I, 6 interactions with chain J, 1 interactions with chain K, 1 interactions with chain G Hydrophobic interactions: I:I.24, I:F.27, I:L.31, I:I.35, I:I.38, J:I.21, J:I.21, J:F.22, J:F.22, J:F.22, J:M.26, K:H.36, G:K.10 CRT.37: 22 residues within 4Å: Chain K: K.10, I.11, L.13 Chain M: L.21, I.24, F.27, Q.28, I.35, I.38 Chain N: E.17, F.18, I.21, F.22, S.25, M.26 Chain O: G.32, L.33, H.36, M.37 Ligands: BCL.35, BCL.36, BCL.39 18 PLIP interactions: 7 interactions with chain M, 2 interactions with chain O, 8 interactions with chain N, 1 interactions with chain K Hydrophobic interactions: M:L.21, M:I.24, M:I.24, M:F.27, M:F.27, M:I.35, M:I.38, O:L.33, O:H.36, N:E.17, N:F.18, N:F.18, N:I.21, N:I.21, N:F.22, N:F.22, N:F.22, K:I.11 CRT.40: 20 residues within 4Å: Chain O: K.10, I.11 Chain Q: I.24, F.27, Q.28, L.31, I.35, I.38 Chain R: E.17, F.18, I.21, F.22, S.25, M.26 Chain S: L.33, H.36, M.37 Ligands: BCL.45, BCL.46, BCL.48 14 PLIP interactions: 5 interactions with chain R, 7 interactions with chain Q, 1 interactions with chain O, 1 interactions with chain S Hydrophobic interactions: R:E.17, R:I.21, R:I.21, R:F.22, R:F.22, Q:I.24, Q:I.24, Q:F.27, Q:F.27, Q:L.31, Q:L.31, Q:I.38, O:I.11, S:H.36 CRT.42: 21 residues within 4Å: Chain M: K.10, I.11, L.13 Chain O: L.21, Q.28, L.31, I.38 Chain P: E.17, F.18, I.21, F.22, S.25, M.26, F.30 Chain Q: G.32, L.33, H.36, M.37 Ligands: BCL.39, BCL.41, BCL.45 19 PLIP interactions: 4 interactions with chain O, 10 interactions with chain P, 2 interactions with chain Q, 3 interactions with chain M Hydrophobic interactions: O:L.21, O:L.31, O:L.31, O:I.38, P:E.17, P:F.18, P:F.18, P:I.21, P:I.21, P:F.22, P:F.22, P:F.22, P:M.26, P:F.30, Q:L.33, Q:H.36, M:K.10, M:I.11, M:L.13 CRT.49: 19 residues within 4Å: Chain Q: K.10, I.11, I.14 Chain S: L.21, I.24, F.27, Q.28, L.31, I.35 Chain T: E.14, E.17, F.18, I.21, F.22 Chain U: L.33, H.36, M.37 Ligands: BCL.50, BCL.52 17 PLIP interactions: 8 interactions with chain T, 7 interactions with chain S, 2 interactions with chain U Hydrophobic interactions: T:E.14, T:F.18, T:F.18, T:I.21, T:F.22, T:F.22, T:F.22, T:F.22, S:L.21, S:I.24, S:I.24, S:F.27, S:F.27, S:L.31, S:L.31, U:L.33, U:H.36 CRT.53: 22 residues within 4Å: Chain U: K.10, I.11, W.12, L.13, I.14 Chain W: L.21, I.24, F.27, Q.28, L.31 Chain X: F.18, I.21, F.22, S.25, M.26, F.30 Chain Y: L.33, H.36, M.37 Ligands: BCL.57, BCL.59, BCL.61 19 PLIP interactions: 6 interactions with chain X, 7 interactions with chain U, 4 interactions with chain W, 2 interactions with chain Y Hydrophobic interactions: X:F.18, X:F.22, X:F.22, X:F.22, X:F.30, X:F.30, U:K.10, U:I.11, U:I.11, U:I.11, U:L.13, U:I.14, U:I.14, W:L.21, W:F.27, W:F.27, W:L.31, Y:L.33, Y:H.36 CRT.55: 18 residues within 4Å: Chain C: F.84 Chain S: I.14 Chain U: L.21, Q.28, I.38 Chain V: E.14, E.17, F.18, I.21, F.22, S.25, M.26 Chain W: G.32, L.33, H.36, M.37 Ligands: BCL.54, BCL.57 12 PLIP interactions: 8 interactions with chain V, 1 interactions with chain W, 1 interactions with chain C, 1 interactions with chain S, 1 interactions with chain U Hydrophobic interactions: V:E.14, V:F.18, V:F.18, V:F.18, V:I.21, V:F.22, V:F.22, V:F.22, C:F.84, S:I.14, U:I.38 Hydrogen bonds: W:M.37 CRT.58: 20 residues within 4Å: Chain 0: G.32, L.33, H.36 Chain W: L.8, K.10, I.11, L.13 Chain Y: I.24, F.27, Q.28, L.31, I.35 Chain Z: E.17, F.18, I.21, F.22, S.25, M.26 Ligands: BCL.61, BCL.64 16 PLIP interactions: 3 interactions with chain W, 4 interactions with chain Y, 8 interactions with chain Z, 1 interactions with chain 0 Hydrophobic interactions: W:L.8, W:I.11, W:L.13, Y:I.24, Y:F.27, Y:L.31, Y:I.35, Z:F.18, Z:F.18, Z:I.21, Z:I.21, Z:F.22, Z:F.22, Z:F.22, Z:F.22, 0:L.33 CRT.65: 20 residues within 4Å: Chain 0: K.10, I.11, L.13, I.14 Chain 2: L.21, I.24, Q.28, L.31, I.35, I.38 Chain 3: F.18, I.21, F.22, M.26 Chain 4: L.33, H.36, M.37 Ligands: BCL.69, BCL.70, BCL.72 14 PLIP interactions: 4 interactions with chain 2, 3 interactions with chain 0, 6 interactions with chain 3, 1 interactions with chain 4 Hydrophobic interactions: 2:L.21, 2:I.24, 2:L.31, 2:I.38, 0:K.10, 0:I.11, 0:L.13, 3:F.18, 3:F.18, 3:I.21, 3:I.21, 3:F.22, 3:M.26, 4:L.33 CRT.67: 18 residues within 4Å: Chain 0: I.35 Chain 1: E.14, A.15, E.17, F.18, I.21, F.22, S.25, M.26 Chain 2: G.32, L.33, H.36, L.40 Chain Y: K.10, I.11 Ligands: BCL.64, BCL.66, BCL.69 11 PLIP interactions: 9 interactions with chain 1, 1 interactions with chain 2, 1 interactions with chain Y Hydrophobic interactions: 1:E.14, 1:F.18, 1:F.18, 1:F.18, 1:I.21, 1:F.22, 1:F.22, 1:F.22, 1:M.26, 2:L.33 Hydrogen bonds: Y:K.10 CRT.73: 21 residues within 4Å: Chain 4: M.4, N.7, L.8, K.10, I.11, L.13, I.14 Chain 6: L.21, I.24, Q.28, L.31, I.35, I.38 Chain 7: F.18, F.22, M.26 Chain 8: L.33, H.36 Ligands: BCL.77, BCL.78, BCL.80 16 PLIP interactions: 8 interactions with chain 6, 2 interactions with chain 4, 4 interactions with chain 7, 2 interactions with chain 8 Hydrophobic interactions: 6:L.21, 6:I.24, 6:I.24, 6:Q.28, 6:L.31, 6:L.31, 6:I.35, 6:I.38, 4:L.8, 4:I.11, 7:F.18, 7:F.18, 7:F.22, 7:F.22, 8:L.33, 8:H.36 CRT.76: 22 residues within 4Å: Chain 2: K.10, I.11, L.13, I.14 Chain 4: L.21, I.24, L.31, I.35, I.38 Chain 5: E.17, F.18, I.21, F.22, S.25, M.26 Chain 6: I.29, L.33, H.36, M.37 Ligands: BCL.72, BCL.74, BCL.77 23 PLIP interactions: 5 interactions with chain 4, 8 interactions with chain 5, 5 interactions with chain 6, 5 interactions with chain 2 Hydrophobic interactions: 4:L.21, 4:I.24, 4:L.31, 4:I.35, 4:I.38, 5:F.18, 5:F.18, 5:F.18, 5:I.21, 5:F.22, 5:F.22, 5:F.22, 5:M.26, 6:I.29, 6:L.33, 6:L.33, 6:H.36, 2:I.11, 2:I.11, 2:I.11, 2:L.13, 2:I.14 Hydrogen bonds: 6:M.37 CRT.81: 18 residues within 4Å: Chain 6: K.10, I.11 Chain 8: L.21, I.24, Q.28, L.31 Chain 9: E.14, E.17, F.18, I.21, F.22, M.26 Chain E: I.29, L.33, H.36, M.37 Ligands: BCL.18, BCL.82 13 PLIP interactions: 3 interactions with chain 8, 7 interactions with chain 9, 2 interactions with chain E, 1 interactions with chain 6 Hydrophobic interactions: 8:L.21, 8:I.24, 8:L.31, 9:F.18, 9:F.18, 9:F.18, 9:I.21, 9:F.22, 9:F.22, 9:F.22, E:I.29, E:L.33, 6:I.11

2 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.16: 6 residues within 4Å: Chain C: Q.5, I.7, F.8, K.42 Chain D: K.204, K.205 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.5, C:I.7 Salt bridges: C:K.42, D:K.204, D:K.204 PEF.43: 11 residues within 4Å: Chain B: V.229 Chain C: I.31, G.32, I.48, W.129 Chain Q: R.19 Chain S: V.22 Ligands: UQ8.8, BCL.10, BCL.11, BPH.12 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain Q Hydrophobic interactions: C:W.129 Hydrogen bonds: Q:R.19

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.17: 3 residues within 4Å: Chain C: H.301 Chain D: S.2, Q.13 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.2, D:S.2, D:Q.13, C:H.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niwa, S. et al., Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 angstrom. Nature (2014)

Release Date

2014-07-09

Peptides

Photosynthetic reaction center cytochrome c subunit: A
Photosynthetic reaction center L subunit: B
Photosynthetic reaction center M subunit: C
Photosynthetic reaction center H subunit: D
LH1 alpha polypeptide: EGIKMOQSUWY02468
LH1 beta polypeptide: FHJLNPRTVXZ13579

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BC

B
BL

C
BM

D
BH

E
BA

G
BD

I
BF

K
BI

M
BK

O
BO

Q
BQ

S
BS

U
BU

W
BW

Y
BY

0
B1

2
B3

4
B5

6
B7

8
B9

F
BB

H
BE

J
BG

L
BJ

N
BN

P
BP

R
BR

T
BT

V
BV

X
BX

Z
BZ

1
B2

3
B4

5
B6

7
B8

9
B0

Membrane

We predict this structure to be a membrane protein.
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Photosynthetic reaction center cytochrome c subunit

Photosynthetic reaction center L subunit

Photosynthetic reaction center M subunit

Photosynthetic reaction center H subunit

LH1 alpha polypeptide

LH1 beta polypeptide

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