SMTL ID : 7vnm.1

Rba sphaeroides PufY-KO RC-LH1 monomer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-13-13-1-mer

Ligands

30 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 28 residues within 4Å: Chain A: F.98, A.125, I.126, A.128, L.132, W.157, V.158, T.161, G.162, Y.163, N.167, F.168, H.169, H.174, A.177, I.178, F.181, S.245, A.246, C.248, M.249 Chain B: T.187, Y.211 Ligands: BPH.2, BCL.5, BCL.7, BCL.9, U10.10 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A, Hydrophobic interactions: B:Y.211, A:F.98, A:F.98, A:A.125, A:T.161, A:Y.163, A:F.168, A:A.177, A:I.178, A:I.178, A:F.181 Hydrogen bonds: A:S.245 Metal complexes: A:H.174 BCL.5: 18 residues within 4Å: Chain A: M.175, I.178, S.179, F.182, T.183, L.186 Chain B: F.91, M.123, W.158, L.161, I.180, H.183, L.184, T.187 Ligands: BCL.1, BPH.6, BCL.9, SPO.11 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:F.91, B:L.161, B:L.184, A:I.178, A:I.178, A:L.186 Metal complexes: B:H.183 Hydrogen bonds: A:T.183 pi-Stacking: A:F.182 BCL.7: 19 residues within 4Å: Chain A: Y.129, L.132, F.147, I.151, W.152, H.154, L.155 Chain B: F.198, G.204, I.207, A.208, Y.211, G.212, L.215 Ligands: BCL.1, BPH.2, BCL.9, U10.10, PC1.13 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:Y.129, A:L.132, A:F.147, A:L.155, B:F.198, B:I.207, B:I.207, B:A.208, B:L.215 Metal complexes: A:H.154 pi-Stacking: B:Y.211 BCL.9: 27 residues within 4Å: Chain A: V.158, Y.163, F.182 Chain B: V.127, F.151, A.154, L.157, W.158, L.161, T.187, N.188, F.190, S.191, L.197, F.198, H.203, S.206, I.207, L.210, Y.211, V.277, G.281, I.285 Ligands: BCL.1, BCL.5, BPH.6, BCL.7 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:V.127, B:F.151, B:L.157, B:W.158, B:T.187, B:F.190, B:L.197, B:I.207, B:I.207, B:I.207, B:L.210, B:Y.211, B:V.277 Salt bridges: B:H.203 BCL.17: 26 residues within 4Å: Chain 0: Y.24, F.49 Chain D: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain E: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain Z: F.4, I.7, Q.20, F.23, I.31 Ligands: PC1.19, BCL.20, SPO.59, BCL.60, SPO.61 18 PLIP interactions: 2 interactions with chain 0, 3 interactions with chain E, 7 interactions with chain Z, 6 interactions with chain D, Hydrophobic interactions: 0:Y.24, 0:F.49, E:A.38, E:V.42, E:W.45, Z:I.7, Z:I.7, Z:Q.20, Z:F.23, Z:F.23, Z:I.31, Z:I.31, D:L.24, D:F.25, D:L.35, D:W.43, D:W.43, D:W.43 BCL.20: 20 residues within 4Å: Chain D: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain E: F.31, S.32, A.35, I.36, H.39, V.42, W.48, F.49 Chain F: W.43 Ligands: BCL.17, SPO.18, BCL.21, SPO.23 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain D, Hydrophobic interactions: E:F.31, E:A.35, E:I.36, E:V.42, E:W.48, E:W.48, E:W.48, E:W.48, E:F.49, E:F.49, D:I.31, D:I.31, D:Y.41 Metal complexes: E:H.39 BCL.21: 25 residues within 4Å: Chain D: F.4, I.7, Q.20, F.23, I.31 Chain E: Y.24, F.49 Chain F: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain G: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.18, BCL.20, SPO.23, BCL.25 17 PLIP interactions: 6 interactions with chain F, 7 interactions with chain D, 2 interactions with chain G, 2 interactions with chain E, Hydrophobic interactions: F:L.24, F:F.25, F:L.35, F:W.43, F:W.43, F:W.43, D:F.4, D:I.7, D:Q.20, D:F.23, D:F.23, D:I.31, D:I.31, G:A.38, G:W.45, E:Y.24, E:F.49 BCL.25: 21 residues within 4Å: Chain F: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain G: F.31, S.32, A.35, I.36, H.39, V.42, Y.43, W.48, F.49 Chain H: W.43 Ligands: BCL.21, SPO.22, SPO.26, BCL.27 14 PLIP interactions: 3 interactions with chain F, 11 interactions with chain G, Hydrophobic interactions: F:I.31, F:I.31, F:Y.41, G:F.31, G:A.35, G:I.36, G:V.42, G:Y.43, G:W.48, G:W.48, G:W.48, G:W.48, G:F.49 Metal complexes: G:H.39 BCL.27: 26 residues within 4Å: Chain F: F.4, I.7, V.16, F.23, I.31 Chain G: Y.24, M.25, F.49 Chain H: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain I: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.22, BCL.25, SPO.26, BCL.28 17 PLIP interactions: 5 interactions with chain F, 8 interactions with chain H, 2 interactions with chain I, 2 interactions with chain G, Hydrophobic interactions: F:I.7, F:V.16, F:F.23, F:I.31, F:I.31, H:L.24, H:F.25, H:L.35, H:W.43, H:W.43, H:W.43, H:W.43, H:W.43, I:A.38, I:W.45, G:Y.24, G:F.49 BCL.28: 20 residues within 4Å: Chain H: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain I: F.31, S.32, A.35, I.36, H.39, V.42, W.48, F.49 Chain J: W.43 Ligands: SPO.24, BCL.27, BCL.30, SPO.32 14 PLIP interactions: 11 interactions with chain I, 3 interactions with chain H, Hydrophobic interactions: I:F.31, I:A.35, I:I.36, I:V.42, I:W.48, I:W.48, I:W.48, I:W.48, I:F.49, I:F.49, H:I.31, H:I.31, H:Y.41 Metal complexes: I:H.39 BCL.30: 26 residues within 4Å: Chain H: I.7, W.8, V.16, Q.20, F.23, I.31 Chain I: Y.24, F.49 Chain J: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain K: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.24, BCL.28, BCL.31, SPO.32 19 PLIP interactions: 3 interactions with chain K, 6 interactions with chain J, 8 interactions with chain H, 2 interactions with chain I, Hydrophobic interactions: K:A.38, K:V.42, K:W.45, J:L.24, J:L.35, J:W.43, J:W.43, J:W.43, J:W.43, H:I.7, H:I.7, H:W.8, H:V.16, H:Q.20, H:F.23, H:I.31, H:I.31, I:Y.24, I:F.49 BCL.31: 21 residues within 4Å: Chain J: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain K: F.31, S.32, A.35, I.36, H.39, V.42, Y.43, W.48, F.49 Chain L: W.43 Ligands: SPO.29, BCL.30, BCL.34, SPO.35 14 PLIP interactions: 2 interactions with chain J, 12 interactions with chain K, Hydrophobic interactions: J:I.31, J:Y.41, K:F.31, K:A.35, K:I.36, K:V.42, K:Y.43, K:W.48, K:W.48, K:W.48, K:W.48, K:F.49, K:F.49 Metal complexes: K:H.39 BCL.34: 24 residues within 4Å: Chain J: I.7, F.23, I.31 Chain K: Y.24, M.25, F.49 Chain L: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain M: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.29, BCL.31, SPO.35, BCL.37 15 PLIP interactions: 6 interactions with chain L, 3 interactions with chain M, 2 interactions with chain K, 4 interactions with chain J, Hydrophobic interactions: L:F.25, L:L.35, L:W.43, L:W.43, L:W.43, L:W.43, M:A.38, M:V.42, M:W.45, K:Y.24, K:F.49, J:I.7, J:F.23, J:I.31, J:I.31 BCL.37: 21 residues within 4Å: Chain L: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain M: F.31, S.32, A.35, I.36, H.39, V.42, Y.43, W.48, F.49 Chain N: W.43 Ligands: SPO.33, BCL.34, BCL.38, SPO.40 14 PLIP interactions: 12 interactions with chain M, 2 interactions with chain L, Hydrophobic interactions: M:F.31, M:A.35, M:I.36, M:V.42, M:Y.43, M:W.48, M:W.48, M:W.48, M:W.48, M:F.49, M:F.49, L:I.31, L:Y.41 Metal complexes: M:H.39 BCL.38: 26 residues within 4Å: Chain L: F.4, I.7, V.16, F.23, I.31 Chain M: H.21, Y.24, M.25, F.49 Chain N: L.24, F.25, A.28, H.32, L.35, W.43 Chain O: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.33, BCL.37, BCL.39, SPO.40 17 PLIP interactions: 6 interactions with chain L, 1 interactions with chain M, 7 interactions with chain N, 3 interactions with chain O, Hydrophobic interactions: L:F.4, L:I.7, L:V.16, L:F.23, L:I.31, L:I.31, M:F.49, N:L.24, N:F.25, N:L.35, N:W.43, N:W.43, N:W.43, N:W.43, O:A.38, O:V.42, O:W.45 BCL.39: 22 residues within 4Å: Chain N: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain O: F.31, S.32, A.35, I.36, H.39, V.42, Y.43, W.48, F.49 Chain P: W.43, L.44 Ligands: SPO.36, BCL.38, SPO.41, BCL.42 16 PLIP interactions: 12 interactions with chain O, 3 interactions with chain N, 1 interactions with chain P, Hydrophobic interactions: O:F.31, O:A.35, O:I.36, O:V.42, O:Y.43, O:W.48, O:W.48, O:W.48, O:W.48, O:F.49, O:F.49, N:I.31, N:I.31, N:Y.41, P:L.44 Metal complexes: O:H.39 BCL.42: 23 residues within 4Å: Chain N: F.23, I.31 Chain O: H.21, Y.24, F.49 Chain P: L.24, F.25, A.28, H.32, L.35, Y.41, W.43 Chain Q: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.36, BCL.39, SPO.41, BCL.45 13 PLIP interactions: 2 interactions with chain O, 3 interactions with chain N, 6 interactions with chain P, 2 interactions with chain Q, Hydrophobic interactions: O:Y.24, O:F.49, N:F.23, N:I.31, N:I.31, P:F.25, P:L.35, P:W.43, P:W.43, P:W.43, P:W.43, Q:A.38, Q:W.45 BCL.45: 21 residues within 4Å: Chain P: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain Q: F.31, S.32, A.35, I.36, H.39, V.42, Y.43, W.48, F.49 Chain R: W.43 Ligands: BCL.42, SPO.44, SPO.46, BCL.47 14 PLIP interactions: 2 interactions with chain P, 12 interactions with chain Q, Hydrophobic interactions: P:I.31, P:Y.41, Q:F.31, Q:A.35, Q:I.36, Q:V.42, Q:Y.43, Q:W.48, Q:W.48, Q:W.48, Q:W.48, Q:F.49, Q:F.49 Metal complexes: Q:H.39 BCL.47: 23 residues within 4Å: Chain P: I.7, V.16, F.23, I.31 Chain Q: H.21, F.49 Chain R: L.24, F.25, A.28, H.32, L.35, W.43 Chain S: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.44, BCL.45, SPO.46, BCL.48 17 PLIP interactions: 7 interactions with chain P, 7 interactions with chain R, 1 interactions with chain Q, 2 interactions with chain S, Hydrophobic interactions: P:I.7, P:V.16, P:F.23, P:F.23, P:F.23, P:I.31, P:I.31, R:L.24, R:F.25, R:L.35, R:W.43, R:W.43, R:W.43, R:W.43, Q:F.49, S:A.38, S:W.45 BCL.48: 21 residues within 4Å: Chain R: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain S: F.31, S.32, A.35, I.36, H.39, V.42, Y.43, W.48, F.49 Chain T: W.43 Ligands: SPO.43, BCL.47, BCL.50, SPO.52 13 PLIP interactions: 10 interactions with chain S, 3 interactions with chain R, Hydrophobic interactions: S:F.31, S:A.35, S:I.36, S:V.42, S:Y.43, S:W.48, S:W.48, S:W.48, S:W.48, R:I.31, R:I.31, R:Y.41 Metal complexes: S:H.39 BCL.50: 26 residues within 4Å: Chain R: F.4, I.7, V.16, F.23, I.31 Chain S: H.21, Y.24, M.25, F.49 Chain T: G.21, L.24, F.25, A.28, H.32, W.43 Chain U: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.43, BCL.48, BCL.51, SPO.52 16 PLIP interactions: 2 interactions with chain S, 5 interactions with chain R, 3 interactions with chain U, 6 interactions with chain T, Hydrophobic interactions: S:Y.24, S:F.49, R:I.7, R:V.16, R:F.23, R:I.31, R:I.31, U:A.38, U:V.42, U:W.45, T:L.24, T:F.25, T:W.43, T:W.43, T:W.43, T:W.43 BCL.51: 19 residues within 4Å: Chain T: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain U: F.31, S.32, A.35, I.36, H.39, V.42, Y.43, W.48, F.49 Ligands: SPO.49, BCL.50, BCL.53 12 PLIP interactions: 11 interactions with chain U, 1 interactions with chain T, Hydrophobic interactions: U:F.31, U:A.35, U:I.36, U:V.42, U:Y.43, U:W.48, U:W.48, U:W.48, U:W.48, U:F.49, T:Y.41 Metal complexes: U:H.39 BCL.53: 20 residues within 4Å: Chain T: W.8, Q.20, F.23, I.31 Chain U: H.21, Y.24, F.49 Chain V: F.25, A.28, H.32, L.35, W.43 Chain W: F.31, V.34, A.35, A.38, H.39 Ligands: SPO.49, BCL.51, BCL.54 14 PLIP interactions: 5 interactions with chain T, 1 interactions with chain W, 6 interactions with chain V, 2 interactions with chain U, Hydrophobic interactions: T:W.8, T:Q.20, T:F.23, T:I.31, T:I.31, W:A.38, V:F.25, V:L.35, V:W.43, V:W.43, V:W.43, V:W.43, U:Y.24, U:F.49 BCL.54: 16 residues within 4Å: Chain V: L.27, A.28, I.31, H.32, L.35, Y.41 Chain W: F.31, S.32, A.35, I.36, H.39, V.42, Y.43, W.48, F.49 Ligands: BCL.53 14 PLIP interactions: 11 interactions with chain W, 3 interactions with chain V, Hydrophobic interactions: W:F.31, W:A.35, W:I.36, W:H.39, W:V.42, W:Y.43, W:Y.43, W:W.48, W:W.48, W:F.49, V:I.31, V:L.35, V:Y.41 pi-Stacking: W:W.48 BCL.55: 21 residues within 4Å: Chain 1: A.24, M.27, M.28, A.31 Chain X: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain Y: G.27, L.30, F.31, V.34, A.35, A.38, H.39, V.42 Ligands: SPO.56, BCL.57 12 PLIP interactions: 6 interactions with chain Y, 4 interactions with chain X, 2 interactions with chain 1, Hydrophobic interactions: Y:L.30, Y:L.30, Y:F.31, Y:F.31, Y:F.31, Y:V.42, X:L.24, X:L.35, X:W.43, X:W.43, 1:M.27, 1:A.31 BCL.57: 21 residues within 4Å: Chain X: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain Y: F.31, S.32, A.35, I.36, H.39, V.42, Y.43, W.48, F.49 Chain Z: W.43 Ligands: BCL.55, SPO.56, BCL.58, SPO.62 14 PLIP interactions: 10 interactions with chain Y, 4 interactions with chain X, Hydrophobic interactions: Y:F.31, Y:A.35, Y:I.36, Y:V.42, Y:Y.43, Y:W.48, Y:W.48, Y:W.48, Y:W.48, X:I.31, X:I.31, X:L.35, X:Y.41 Metal complexes: Y:H.39 BCL.58: 23 residues within 4Å: Chain 0: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain X: I.7, Q.20, I.31 Chain Y: Y.24, F.49 Chain Z: L.24, F.25, A.28, H.32, L.35, W.43 Ligands: SPO.56, BCL.57, SPO.59, BCL.60, SPO.62 11 PLIP interactions: 1 interactions with chain Y, 2 interactions with chain 0, 5 interactions with chain Z, 3 interactions with chain X, Hydrophobic interactions: Y:F.49, 0:A.38, 0:W.45, Z:L.24, Z:L.35, Z:W.43, Z:W.43, Z:W.43, X:I.7, X:I.31, X:I.31 BCL.60: 20 residues within 4Å: Chain 0: F.31, S.32, A.35, I.36, H.39, V.42, W.48, F.49 Chain D: W.43 Chain Z: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Ligands: BCL.17, BCL.58, SPO.59, SPO.61 12 PLIP interactions: 3 interactions with chain Z, 9 interactions with chain 0, Hydrophobic interactions: Z:I.31, Z:I.31, Z:Y.41, 0:F.31, 0:A.35, 0:I.36, 0:V.42, 0:W.48, 0:W.48, 0:W.48, 0:W.48 Metal complexes: 0:H.39 BCL.64: 19 residues within 4Å: Chain 2: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain 3: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain V: V.16, Q.20, F.23, I.31 Ligands: BCL.65 12 PLIP interactions: 2 interactions with chain 3, 7 interactions with chain 2, 3 interactions with chain V, Hydrophobic interactions: 3:A.38, 3:W.45, 2:F.25, 2:A.28, 2:L.35, 2:W.43, 2:W.43, V:V.16, V:F.23, V:I.31 pi-Stacking: 2:H.32 Metal complexes: 2:H.32 BCL.65: 12 residues within 4Å: Chain 2: L.24, L.27, A.28, I.31, Y.41 Chain 3: F.31, A.35, H.39, V.42, W.48, F.49 Ligands: BCL.64 9 PLIP interactions: 7 interactions with chain 3, 2 interactions with chain 2, Hydrophobic interactions: 3:F.31, 3:A.35, 3:V.42, 3:W.48, 3:W.48, 3:W.48, 2:I.31, 2:I.31 Metal complexes: 3:H.39

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.2: 23 residues within 4Å: Chain A: T.39, F.42, A.43, G.46, A.97, F.98, W.101, E.105, I.118, A.121, F.122, A.125, Y.149, V.242 Chain B: Y.211, A.214, L.215, M.219, W.253, M.257 Ligands: BCL.1, BCL.7, U10.10 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:Y.211, B:A.214, B:L.215, A:A.43, A:A.97, A:A.121, A:F.122, A:F.122, A:F.122, A:A.125, A:Y.149, A:V.242, A:V.242 BPH.6: 23 residues within 4Å: Chain A: F.182, A.185, L.186, A.189, L.190, L.220, V.221 Chain B: S.60, G.64, W.67, F.68, A.126, V.127, W.130, T.134, T.147, A.150, F.151, A.154, A.274, T.278 Ligands: BCL.5, BCL.9 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.67, B:F.68, B:A.126, B:W.130, B:A.150, B:F.151, B:F.151, B:F.151, B:A.154, A:A.185, A:A.189, A:L.190

7 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.3: 9 residues within 4Å: Chain A: A.51, T.59, W.60, N.61, I.65 Chain F: L.33, L.36, S.37 Ligands: PC1.13 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain A Hydrophobic interactions: F:L.33, A:I.65 Hydrogen bonds: A:T.59, A:W.60, A:N.61 PC1.13: 20 residues within 4Å: Chain A: I.50, N.61, P.62, Q.63, Y.149, I.151, W.152 Chain B: P.201, L.205, A.208, W.298, H.302, G.303, M.304 Chain C: N.9, I.17, Y.18, W.21 Ligands: PC1.3, BCL.7 13 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: A:I.50, A:Q.63, A:I.151, A:W.152, B:P.201, B:L.205, B:A.208, C:I.17, C:W.21 Salt bridges: B:H.302 Hydrogen bonds: C:N.9, C:N.9, C:Y.18 PC1.14: 13 residues within 4Å: Chain B: M.257, G.258, F.259 Chain C: I.28, Q.32, M.36, Y.40, Q.53, G.54, P.55, F.56 Ligands: U10.10, PC1.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.259, B:F.259, C:I.28 PC1.15: 14 residues within 4Å: Chain C: A.51, N.52, Q.53, G.54, P.55 Chain D: F.11, R.15, V.16 Chain F: D.12, R.14, R.15, V.18, A.19 Ligands: PC1.16 11 PLIP interactions: 4 interactions with chain C, 5 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: C:P.55, F:V.18, F:A.19, D:F.11 Hydrogen bonds: C:A.51, C:Q.53, C:G.54 Salt bridges: F:D.12, F:R.14, F:R.15, D:R.15 PC1.16: 12 residues within 4Å: Chain A: G.28, P.29, F.30 Chain C: L.42, N.52, G.54, P.55 Chain D: R.15 Ligands: U10.10, PC1.14, PC1.15, PC1.19 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.15 Hydrophobic interactions: C:P.55 PC1.19: 18 residues within 4Å: Chain A: A.2, V.27, F.40 Chain C: N.44, A.51, N.52, E.94 Chain D: D.12, R.14, R.15, V.18, A.19, G.21, V.22, F.25 Chain Z: R.15 Ligands: PC1.16, BCL.17 9 PLIP interactions: 2 interactions with chain Z, 1 interactions with chain A, 5 interactions with chain D, 1 interactions with chain C Salt bridges: Z:R.15, Z:R.15, D:D.12, D:R.14, D:R.15, C:E.94 Hydrophobic interactions: A:F.40, D:V.18, D:A.19 PC1.63: 12 residues within 4Å: Chain 1: K.29, G.30, W.33, V.37 Chain A: T.16, L.17, V.18, G.19, F.35 Chain X: R.15, V.18, V.22 8 PLIP interactions: 2 interactions with chain A, 5 interactions with chain 1, 1 interactions with chain X Hydrophobic interactions: A:F.35, 1:W.33, 1:W.33, 1:V.37, 1:V.37 Hydrogen bonds: A:G.19 Salt bridges: 1:K.29, X:R.15

2 x U10: UBIQUINONE-10(Non-covalent)

U10.4: 16 residues within 4Å: Chain A: I.176, S.179, F.180, T.183, L.190, H.191, L.194, E.213, D.214, F.217, S.224, I.225, G.226, T.227, I.230, L.233 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.176, A:L.190, A:F.217, A:F.217, A:F.217, A:I.225, A:I.230, A:I.230, A:L.233 Hydrogen bonds: A:I.225, A:G.226 U10.10: 27 residues within 4Å: Chain A: V.27, F.30, V.32, G.36, V.37, F.40, W.101, R.104 Chain B: M.219, H.220, T.223, I.224, A.249, A.250, W.253, M.257, F.259, N.260, A.261, T.262, I.266, W.269 Ligands: BCL.1, BPH.2, BCL.7, PC1.14, PC1.16 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:W.253, B:M.257, B:F.259, B:F.259, B:A.261, B:I.266, B:I.266, B:W.269, A:V.27, A:F.30, A:F.30, A:F.30, A:V.32, A:V.32, A:V.37, A:F.40, A:F.40, A:W.101 Hydrogen bonds: B:A.261

1 x FE2: FE (II) ION(Non-covalent)

FE2.8: 5 residues within 4Å: Chain A: H.191, H.231 Chain B: H.220, E.235, H.267 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.220, B:E.235, B:H.267, A:H.191, A:H.231

22 x SPO: SPHEROIDENE(Non-covalent)

SPO.11: 24 residues within 4Å: Chain B: F.68, F.69, I.71, G.72, I.73, F.75, W.76, F.86, F.106, S.120, F.121, M.123, F.124, W.158, L.161, G.162, F.163, W.172, V.176, Y.178, G.179, H.183 Chain N: M.30 Ligands: BCL.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.68, B:F.68, B:F.68, B:F.69, B:I.71, B:I.71, B:I.73, B:F.75, B:F.86, B:F.106, B:F.121, B:F.121, B:F.124, B:W.158, B:L.161, B:F.163, B:F.163, B:W.172, B:V.176 SPO.18: 26 residues within 4Å: Chain D: F.17, Q.20, F.23, L.24, L.27, M.30 Chain E: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain F: F.25, A.28, V.29, H.32, L.33 Chain Z: K.6, I.7, M.9, I.10 Ligands: BCL.20, BCL.21, SPO.23, SPO.61 18 PLIP interactions: 6 interactions with chain Z, 6 interactions with chain E, 2 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: Z:K.6, Z:K.6, Z:I.7, Z:M.9, Z:I.10, Z:I.10, E:E.19, E:L.20, E:V.23, E:L.28, E:L.28, E:F.31, F:A.28, F:V.29, D:F.23, D:L.24, D:L.27, D:L.27 SPO.22: 23 residues within 4Å: Chain D: K.6, I.7, I.10 Chain F: F.17, Q.20, F.23, L.24, L.27, M.30 Chain G: E.19, V.23, G.27, L.28, F.31 Chain H: F.25, A.28, V.29, H.32, L.33 Ligands: SPO.23, BCL.25, SPO.26, BCL.27 16 PLIP interactions: 4 interactions with chain F, 3 interactions with chain H, 5 interactions with chain G, 4 interactions with chain D Hydrophobic interactions: F:F.23, F:L.24, F:L.27, F:L.27, H:F.25, H:A.28, H:V.29, G:E.19, G:V.23, G:L.28, G:L.28, G:F.31, D:K.6, D:K.6, D:I.10, D:I.10 SPO.23: 14 residues within 4Å: Chain E: F.49 Chain F: F.17, Q.20, G.21 Chain G: V.34, A.38, A.41, V.42, I.44, W.45 Ligands: SPO.18, BCL.20, BCL.21, SPO.22 8 PLIP interactions: 6 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:V.34, G:A.38, G:A.41, G:V.42, G:I.44, G:W.45, F:F.17, F:F.17 SPO.24: 27 residues within 4Å: Chain F: K.3, F.4, K.6, I.7, I.10 Chain G: L.7 Chain H: F.17, Q.20, F.23, L.24, L.27, M.30, I.34 Chain I: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain J: A.28, H.32, L.33 Ligands: SPO.26, BCL.28, BCL.30, SPO.32 15 PLIP interactions: 1 interactions with chain G, 5 interactions with chain I, 5 interactions with chain H, 1 interactions with chain J, 3 interactions with chain F Hydrophobic interactions: G:L.7, I:E.19, I:V.23, I:L.28, I:L.28, I:F.31, H:F.23, H:L.24, H:L.27, H:L.27, H:I.34, J:A.28, F:F.4, F:K.6, F:I.10 SPO.26: 13 residues within 4Å: Chain G: Y.43, F.49 Chain H: F.17, Q.20 Chain I: F.31, V.34, A.38, V.42, W.45 Ligands: SPO.22, SPO.24, BCL.25, BCL.27 7 PLIP interactions: 1 interactions with chain H, 5 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: H:F.17, I:F.31, I:V.34, I:A.38, I:V.42, I:W.45, G:F.49 SPO.29: 22 residues within 4Å: Chain H: K.3, F.4, K.6, I.7, I.10 Chain J: Q.20, F.23, L.24, L.27, I.31 Chain K: L.20, V.23, Y.24, G.27, L.28 Chain L: A.28, H.32, L.33, L.36 Ligands: BCL.31, SPO.32, BCL.34 16 PLIP interactions: 5 interactions with chain J, 5 interactions with chain K, 4 interactions with chain H, 2 interactions with chain L Hydrophobic interactions: J:F.23, J:F.23, J:L.24, J:L.27, J:I.31, K:L.20, K:L.20, K:L.20, K:V.23, K:L.28, H:K.6, H:I.7, H:I.7, H:I.10, L:A.28, L:L.36 SPO.32: 15 residues within 4Å: Chain I: Y.43, F.49 Chain J: F.17, Q.20, K.50, Y.51 Chain K: V.34, A.38, A.41, V.42, W.45 Ligands: SPO.24, BCL.28, SPO.29, BCL.30 7 PLIP interactions: 4 interactions with chain K, 3 interactions with chain I Hydrophobic interactions: K:V.34, K:A.38, K:A.41, K:V.42, I:F.49, I:F.49, I:F.49 SPO.33: 23 residues within 4Å: Chain J: F.4, K.6, I.7, I.10 Chain L: Q.20, F.23, L.24, L.27, M.30 Chain M: L.20, V.23, Y.24, G.27, L.28, F.31 Chain N: F.25, A.28, V.29, H.32, L.36 Ligands: SPO.35, BCL.37, BCL.38 18 PLIP interactions: 4 interactions with chain L, 6 interactions with chain M, 4 interactions with chain N, 4 interactions with chain J Hydrophobic interactions: L:F.23, L:F.23, L:L.27, L:L.27, M:L.20, M:L.20, M:V.23, M:L.28, M:L.28, M:F.31, N:F.25, N:A.28, N:V.29, N:L.36, J:F.4, J:K.6, J:I.7, J:I.10 SPO.35: 13 residues within 4Å: Chain K: F.49 Chain L: F.17, Q.20, K.50 Chain M: V.34, A.38, A.41, V.42, I.44, W.45 Ligands: BCL.31, SPO.33, BCL.34 8 PLIP interactions: 1 interactions with chain L, 6 interactions with chain M, 1 interactions with chain K Hydrophobic interactions: L:F.17, M:V.34, M:A.38, M:A.41, M:V.42, M:I.44, M:W.45, K:F.49 SPO.36: 28 residues within 4Å: Chain L: K.3, F.4, K.6, I.7 Chain M: L.7 Chain N: F.17, Q.20, F.23, L.24, L.27, M.30, I.31, I.34 Chain O: L.20, V.23, Y.24, G.27, L.28 Chain P: F.25, A.28, V.29, H.32, L.33, W.43 Ligands: BCL.39, SPO.40, SPO.41, BCL.42 17 PLIP interactions: 7 interactions with chain N, 1 interactions with chain L, 4 interactions with chain P, 4 interactions with chain O, 1 interactions with chain M Hydrophobic interactions: N:F.23, N:L.24, N:L.24, N:L.27, N:L.27, N:I.31, N:I.34, L:K.6, P:F.25, P:A.28, P:V.29, P:W.43, O:L.20, O:L.20, O:L.20, O:L.28, M:L.7 SPO.40: 12 residues within 4Å: Chain M: F.49 Chain N: F.17 Chain O: F.31, V.34, A.38, A.41, V.42, I.44, W.45 Ligands: SPO.36, BCL.37, BCL.38 8 PLIP interactions: 2 interactions with chain M, 5 interactions with chain O, 1 interactions with chain N Hydrophobic interactions: M:F.49, M:F.49, O:F.31, O:A.38, O:A.41, O:V.42, O:I.44, N:F.17 SPO.41: 12 residues within 4Å: Chain O: Y.43, F.49 Chain P: Y.51 Chain Q: V.34, A.38, A.41, V.42, W.45 Ligands: SPO.36, BCL.39, BCL.42, SPO.44 5 PLIP interactions: 2 interactions with chain O, 3 interactions with chain Q Hydrophobic interactions: O:F.49, O:F.49, Q:V.34, Q:A.41, Q:W.45 SPO.43: 26 residues within 4Å: Chain P: K.3, F.4, K.6, I.7, I.10 Chain R: Q.20, F.23, L.24, L.27, M.30, I.31 Chain S: E.19, L.20, V.23, G.27, L.28, F.31 Chain T: F.25, A.28, V.29, H.32, L.33 Ligands: SPO.46, BCL.48, BCL.50, SPO.52 20 PLIP interactions: 5 interactions with chain R, 3 interactions with chain T, 7 interactions with chain S, 5 interactions with chain P Hydrophobic interactions: R:F.23, R:L.24, R:L.27, R:L.27, R:I.31, T:F.25, T:A.28, T:V.29, S:E.19, S:L.20, S:V.23, S:L.28, S:L.28, S:L.28, S:F.31, P:K.6, P:I.7, P:I.7, P:I.10, P:I.10 SPO.44: 26 residues within 4Å: Chain N: F.4, K.6, I.7, I.10 Chain P: F.17, Q.20, F.23, L.24, L.27, M.30, I.31 Chain Q: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain R: F.25, A.28, V.29, H.32, L.33 Ligands: SPO.41, BCL.45, BCL.47 22 PLIP interactions: 6 interactions with chain P, 3 interactions with chain R, 6 interactions with chain N, 7 interactions with chain Q Hydrophobic interactions: P:F.17, P:F.23, P:L.24, P:L.27, P:L.27, P:I.31, R:F.25, R:A.28, R:V.29, N:F.4, N:K.6, N:K.6, N:I.7, N:I.10, N:I.10, Q:E.19, Q:L.20, Q:V.23, Q:V.23, Q:L.28, Q:L.28, Q:F.31 SPO.46: 10 residues within 4Å: Chain Q: F.49 Chain R: F.17, K.50 Chain S: V.34, A.38, A.41, W.45 Ligands: SPO.43, BCL.45, BCL.47 7 PLIP interactions: 3 interactions with chain S, 3 interactions with chain Q, 1 interactions with chain R Hydrophobic interactions: S:A.38, S:A.41, S:W.45, Q:F.49, Q:F.49, Q:F.49, R:F.17 SPO.49: 24 residues within 4Å: Chain R: K.3, F.4, K.6, I.7, I.10 Chain T: F.17, Q.20, F.23, L.24, L.27, M.30, I.31, I.34 Chain U: L.20, V.23, G.27, L.28, F.31 Chain V: F.25, A.28, H.32 Ligands: BCL.51, SPO.52, BCL.53 18 PLIP interactions: 7 interactions with chain T, 2 interactions with chain V, 5 interactions with chain U, 4 interactions with chain R Hydrophobic interactions: T:F.17, T:F.23, T:L.24, T:L.24, T:L.27, T:L.27, T:I.31, V:F.25, V:A.28, U:L.20, U:V.23, U:L.28, U:L.28, U:F.31, R:F.4, R:K.6, R:I.7, R:I.10 SPO.52: 11 residues within 4Å: Chain S: Y.43, F.49 Chain T: Q.20, Y.51 Chain U: A.38, V.42, W.45 Ligands: SPO.43, BCL.48, SPO.49, BCL.50 6 PLIP interactions: 1 interactions with chain S, 5 interactions with chain U Hydrophobic interactions: S:F.49, U:A.38, U:V.42, U:W.45, U:W.45, U:W.45 SPO.56: 19 residues within 4Å: Chain 1: R.20, V.23, M.27 Chain X: Q.20, L.24, L.27, M.30 Chain Y: V.23, Y.24, G.27, L.28 Chain Z: F.25, A.28, V.29, H.32, L.33 Ligands: BCL.55, BCL.57, BCL.58 11 PLIP interactions: 4 interactions with chain Y, 2 interactions with chain 1, 3 interactions with chain X, 2 interactions with chain Z Hydrophobic interactions: Y:V.23, Y:L.28, Y:L.28, Y:L.28, 1:R.20, 1:V.23, X:L.24, X:L.27, X:L.27, Z:A.28, Z:V.29 SPO.59: 27 residues within 4Å: Chain 0: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain D: F.25, A.28, V.29, H.32, L.33 Chain X: F.4, K.6, I.10 Chain Y: L.7 Chain Z: F.17, Q.20, F.23, L.24, L.27, M.30 Ligands: BCL.17, BCL.58, BCL.60, SPO.61, SPO.62 19 PLIP interactions: 3 interactions with chain D, 7 interactions with chain 0, 4 interactions with chain X, 1 interactions with chain Y, 4 interactions with chain Z Hydrophobic interactions: D:F.25, D:A.28, D:V.29, 0:E.19, 0:L.20, 0:L.20, 0:V.23, 0:L.28, 0:L.28, 0:F.31, X:F.4, X:F.4, X:K.6, X:I.10, Y:L.7, Z:F.17, Z:F.23, Z:L.27, Z:L.27 SPO.61: 14 residues within 4Å: Chain 0: Y.43, F.49 Chain D: F.17, Q.20, Y.51 Chain E: V.34, A.38, A.41, V.42, W.45 Ligands: BCL.17, SPO.18, SPO.59, BCL.60 8 PLIP interactions: 4 interactions with chain 0, 3 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: 0:F.49, 0:F.49, 0:F.49, E:A.41, E:V.42, E:W.45 Hydrogen bonds: 0:Y.43, D:Y.51 SPO.62: 12 residues within 4Å: Chain 0: F.31, V.34, A.38, A.41, I.44, W.45 Chain Y: F.49 Chain Z: F.17, Q.20 Ligands: BCL.57, BCL.58, SPO.59 8 PLIP interactions: 5 interactions with chain 0, 2 interactions with chain Y, 1 interactions with chain Z Hydrophobic interactions: 0:F.31, 0:V.34, 0:A.41, 0:I.44, 0:W.45, Y:F.49, Y:F.49, Z:F.17

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 20 residues within 4Å: Chain A: N.200, P.201 Chain B: G.144, K.145, H.146, W.149, S.153, W.156, R.268, I.271, W.272, L.279, I.283 Chain C: L.15, S.19, I.22, F.23, G.26, L.27, Y.30 26 PLIP interactions: 9 interactions with chain C, 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:L.15, C:I.22, C:F.23, C:F.23, C:F.23, C:F.23, C:L.27, C:Y.30, B:W.149, B:W.156, B:W.156, B:W.156, B:W.156, B:W.156, B:I.271, B:L.279, B:I.283 Hydrogen bonds: C:Y.30, B:K.145, B:R.268, A:N.200 Salt bridges: B:H.146, B:H.146, B:H.146, B:R.268, B:R.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, P. et al., Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex. Nat Commun (2022)

Release Date

2022-05-04

Peptides

Reaction center protein L chain: A
Reaction center protein M chain: B
Reaction center protein H chain: C
Light-harvesting protein B-875 alpha chain: DFHJLNPRTVXZ2
Light-harvesting protein B-875 beta chain: EGIKMOQSUWY03
Intrinsic membrane protein PufX: 1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
M

C
H

D
A

F
D

H
F

J
I

L
K

N
O

P
Q

R
S

T
U

V
W

X
7

Z
9

2
1

E
B

G
E

I
G

K
J

M
N

O
P

Q
R

S
T

U
V

W
C

Y
8

0
0

3
2

1
X

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Reaction center protein L chain

Reaction center protein M chain

Reaction center protein H chain

Light-harvesting protein B-875 alpha chain

Light-harvesting protein B-875 beta chain

Intrinsic membrane protein PufX

Related Entries With Identical Sequence