SMTL ID : 7yml.1

Structure of photosynthetic LH1-RC super-complex of Rhodobacter capsulatus

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-10-10-1-mer

Ligands

25 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 29 residues within 4Å: Chain A: F.98, A.125, I.126, A.128, Y.129, L.132, W.157, V.158, T.161, G.162, Y.163, N.167, F.168, H.169, H.174, G.177, I.178, F.181, F.182, S.245, A.246, C.248, M.249 Chain B: T.185, Y.209 Ligands: BPH.2, BCL.10, BCL.14, BCL.15 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.98, A:F.98, A:V.158, A:T.161, A:Y.163, A:F.168, A:I.178, A:I.178, A:F.181, A:F.181, A:F.182, B:Y.209 Metal complexes: A:H.174 BCL.10: 20 residues within 4Å: Chain A: Y.129, L.132, F.147, I.151, W.152, H.154, L.155, V.158 Chain B: F.196, G.202, I.205, A.206, Y.209, G.210, L.213 Ligands: BCL.1, BPH.2, PGV.13, BCL.15, U10.18 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:Y.129, A:L.132, A:F.147, A:L.155, A:V.158, B:F.196, B:I.205, B:I.205, B:Y.209, B:L.213 pi-Stacking: A:F.147, B:Y.209 Metal complexes: A:H.154 BCL.14: 25 residues within 4Å: Chain A: H.169, M.175, I.178, S.179, F.182, T.183, W.186, M.221 Chain B: I.50, M.121, W.128, W.156, L.159, I.178, H.181, L.182, T.185 Ligands: BCL.1, U10.3, BCL.15, BPH.16, SPO.19, LDA.27, LDA.29, LDA.30 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:I.50, B:W.128, B:W.128, B:L.159, B:I.178, B:L.182, B:T.185, A:I.178, A:I.178, A:W.186, A:W.186 Metal complexes: B:H.181 BCL.15: 29 residues within 4Å: Chain A: V.158, Y.163, H.169, F.182 Chain B: M.121, V.125, F.149, A.152, L.155, W.156, L.159, W.184, T.185, N.186, F.188, S.189, L.195, F.196, H.201, S.204, I.205, Y.209, V.275, G.279, I.283 Ligands: BCL.1, BCL.10, BCL.14, BPH.16 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.125, B:V.125, B:F.149, B:A.152, B:L.155, B:W.156, B:W.156, B:W.184, B:T.185, B:F.188, B:F.196, B:F.196, B:I.205, B:Y.209, B:V.275 Metal complexes: B:H.201 pi-Cation interactions: A:H.169 BCL.36: 18 residues within 4Å: Chain D: 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 Chain X: G.23, M.26, A.30 Ligands: BCL.38, SPO.39, LMT.89 10 PLIP interactions: 2 interactions with chain X, 6 interactions with chain D, 2 interactions with chain E, Hydrophobic interactions: X:M.26, X:A.30, D:L.24, D:A.28, D:L.35, D:W.43, D:W.43, E:A.38 Metal complexes: D:H.32 Hydrogen bonds: E:H.39 BCL.38: 19 residues within 4Å: Chain D: L.24, L.27, A.28, I.31, H.32, F.41 Chain E: F.31, I.32, A.35, H.39, V.42, M.43, W.48, F.49 Chain F: W.43 Ligands: BCL.36, SPO.39, BCL.40, SPO.44 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain D, Hydrophobic interactions: E:A.35, E:H.39, E:V.42, E:W.48, E:W.48, E:W.48, E:F.49, E:F.49, D:I.31, D:I.31, D:F.41 Metal complexes: E:H.39 BCL.40: 24 residues within 4Å: Chain D: F.4, Q.20, I.31 Chain E: H.21, Y.24, F.49 Chain F: 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: U10.4, BCL.38, SPO.39, SPO.44, BCL.45 19 PLIP interactions: 3 interactions with chain G, 10 interactions with chain F, 4 interactions with chain D, 2 interactions with chain E, Hydrophobic interactions: G:A.38, G:V.42, G:W.45, F:L.24, F:F.25, F:L.35, F:W.43, F:W.43, F:W.43, F:W.43, D:F.4, D:Q.20, D:I.31, D:I.31, E:Y.24, E:F.49 pi-Stacking: F:H.32, F:H.32 Metal complexes: F:H.32 BCL.45: 20 residues within 4Å: Chain F: L.24, L.27, A.28, I.31, H.32, L.35 Chain G: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Chain H: W.43 Ligands: BCL.40, SPO.41, BCL.48, SPO.49 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain F, Hydrophobic interactions: G:F.31, G:I.32, G:A.35, G:V.36, G:V.42, G:W.48, G:W.48, G:W.48, G:F.49, G:F.49, F:I.31 Metal complexes: G:H.39 BCL.46: 24 residues within 4Å: Chain C: N.52, P.55 Chain H: F.11, R.15, A.19, F.23 Chain J: V.18, A.19, V.22, F.23, F.25, L.26, L.27, V.29, L.30, L.33 Chain L: F.25 Ligands: PGV.5, LMT.11, PGV.34, PGV.35, MYR.47, BCL.53, LMT.57 19 PLIP interactions: 11 interactions with chain J, 1 interactions with chain L, 6 interactions with chain H, 1 interactions with chain C, Hydrophobic interactions: J:V.18, J:V.18, J:V.22, J:V.22, J:F.23, J:F.25, J:L.26, J:L.26, J:V.29, J:L.30, J:L.33, L:F.25, H:F.11, H:R.15, H:F.23 Salt bridges: H:R.15 pi-Cation interactions: H:R.15, H:R.15 Hydrogen bonds: C:N.52 BCL.48: 25 residues within 4Å: Chain F: I.7, Q.20, F.23, I.31 Chain G: Y.24, M.25, F.49 Chain H: 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.41, SPO.43, BCL.45, SPO.49, BCL.50 18 PLIP interactions: 9 interactions with chain H, 3 interactions with chain I, 5 interactions with chain F, 1 interactions with chain G, Hydrophobic interactions: H:F.25, H:L.35, H:W.43, H:W.43, H:W.43, H:W.43, I:A.38, I:V.42, I:W.45, F:I.7, F:F.23, F:F.23, F:I.31, F:I.31, G:F.49 pi-Stacking: H:H.32, H:H.32 Metal complexes: H:H.32 BCL.50: 20 residues within 4Å: Chain H: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain I: F.31, I.32, A.35, H.39, V.42, M.43, W.48, F.49 Chain J: W.43 Ligands: SPO.43, BCL.48, SPO.51, BCL.53 14 PLIP interactions: 11 interactions with chain I, 3 interactions with chain H, Hydrophobic interactions: I:F.31, I:I.32, I:A.35, 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:L.35, H:F.41 Metal complexes: I:H.39 BCL.53: 29 residues within 4Å: Chain H: F.4, W.8, V.16, Q.20, F.23, I.31 Chain I: H.21, Y.24, M.25, 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.43, BCL.46, BCL.50, SPO.51, BCL.56 22 PLIP interactions: 8 interactions with chain H, 2 interactions with chain I, 9 interactions with chain J, 3 interactions with chain K, Hydrophobic interactions: H:F.4, H:W.8, H:V.16, H:Q.20, H:F.23, H:F.23, H:I.31, H:I.31, I:Y.24, I:F.49, J:F.25, J:L.35, J:W.43, J:W.43, J:W.43, J:W.43, K:A.38, K:V.42, K:W.45 pi-Stacking: J:H.32, J:H.32 Metal complexes: J:H.32 BCL.56: 20 residues within 4Å: Chain J: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain K: F.31, I.32, A.35, H.39, V.42, M.43, W.48, F.49 Chain L: W.43 Ligands: BCL.53, SPO.54, BCL.58, SPO.59 14 PLIP interactions: 10 interactions with chain K, 4 interactions with chain J, Hydrophobic interactions: K:F.31, K:I.32, K:A.35, K:V.42, K:W.48, K:W.48, K:W.48, K:F.49, K:F.49, J:I.31, J:I.31, J:L.35, J:F.41 Metal complexes: K:H.39 BCL.58: 26 residues within 4Å: Chain J: F.4, W.8, V.16, 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.54, BCL.56, SPO.59, BCL.60 19 PLIP interactions: 6 interactions with chain J, 3 interactions with chain M, 9 interactions with chain L, 1 interactions with chain K, Hydrophobic interactions: J:F.4, J:W.8, J:V.16, J:F.23, J:I.31, J:I.31, M:A.38, M:V.42, M:W.45, L:F.25, L:L.35, L:W.43, L:W.43, L:W.43, L:W.43, K:F.49 pi-Stacking: L:H.32, L:H.32 Metal complexes: L:H.32 BCL.60: 21 residues within 4Å: Chain L: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain M: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Chain N: W.43 Ligands: SPO.55, BCL.58, BCL.62, SPO.65 15 PLIP interactions: 3 interactions with chain L, 12 interactions with chain M, Hydrophobic interactions: L:I.31, L:L.35, L:F.41, M:F.31, M:I.32, M:A.35, M:V.36, M:V.42, M:W.48, M:W.48, M:W.48, M:W.48, M:F.49, M:F.49 Metal complexes: M:H.39 BCL.62: 24 residues within 4Å: Chain L: I.7, V.16, F.23, I.31 Chain M: H.21, Y.24, 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.55, BCL.60, SPO.65, BCL.66 17 PLIP interactions: 5 interactions with chain L, 3 interactions with chain O, 8 interactions with chain N, 1 interactions with chain M, Hydrophobic interactions: L:I.7, L:V.16, L:F.23, L:I.31, L:I.31, O:A.38, O:V.42, O:W.45, N:F.25, N:L.35, N:W.43, N:W.43, N:W.43, N:W.43, M:F.49 pi-Stacking: N:H.32 Metal complexes: N:H.32 BCL.66: 21 residues within 4Å: Chain N: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain O: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Chain P: W.43 Ligands: BCL.62, SPO.63, BCL.71, SPO.72 14 PLIP interactions: 10 interactions with chain O, 4 interactions with chain N, Hydrophobic interactions: O:F.31, O:I.32, O:A.35, O:V.36, O:V.42, O:W.48, O:W.48, O:W.48, O:F.49, N:I.31, N:I.31, N:L.35, N:F.41 Metal complexes: O:H.39 BCL.71: 22 residues within 4Å: Chain N: V.16, F.23, I.31 Chain O: H.21, Y.24, F.49 Chain P: L.24, F.25, A.28, H.32, W.43 Chain Q: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.63, BCL.66, SPO.72, BCL.73 17 PLIP interactions: 5 interactions with chain N, 3 interactions with chain Q, 8 interactions with chain P, 1 interactions with chain O, Hydrophobic interactions: N:V.16, N:F.23, N:F.23, N:I.31, N:I.31, Q:A.38, Q:V.42, Q:W.45, P:F.25, P:W.43, P:W.43, P:W.43, P:W.43, O:F.49 pi-Stacking: P:H.32, P:H.32 Metal complexes: P:H.32 BCL.73: 21 residues within 4Å: Chain P: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain Q: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Chain R: W.43 Ligands: SPO.64, BCL.71, BCL.76, SPO.79 13 PLIP interactions: 11 interactions with chain Q, 2 interactions with chain P, Hydrophobic interactions: Q:F.31, Q:I.32, Q:A.35, Q:V.36, Q:V.42, Q:W.48, Q:W.48, Q:W.48, Q:W.48, Q:F.49, P:I.31, P:F.41 Metal complexes: Q:H.39 BCL.76: 24 residues within 4Å: Chain P: V.16, F.23, I.31 Chain Q: Y.24, 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.64, PGV.69, BCL.73, SPO.77, SPO.79, BCL.80 15 PLIP interactions: 7 interactions with chain R, 4 interactions with chain P, 2 interactions with chain S, 2 interactions with chain Q, Hydrophobic interactions: R:F.25, R:L.35, R:W.43, R:W.43, R:W.43, R:W.43, P:V.16, P:F.23, P:I.31, P:I.31, S:A.38, S:W.45, Q:Y.24, Q:F.49 Metal complexes: R:H.32 BCL.80: 20 residues within 4Å: Chain R: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain S: F.31, I.32, A.35, H.39, V.42, M.43, W.48, F.49 Chain T: W.43 Ligands: BCL.76, SPO.77, BCL.81, SPO.82 12 PLIP interactions: 2 interactions with chain R, 10 interactions with chain S, Hydrophobic interactions: R:I.31, R:F.41, S:F.31, S:I.32, S:A.35, S:V.42, S:W.48, S:W.48, S:W.48, S:F.49, S:F.49 Metal complexes: S:H.39 BCL.81: 23 residues within 4Å: Chain R: V.16, F.23, I.31 Chain S: H.21, Y.24, M.25, F.49 Chain T: 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.77, BCL.80, SPO.82, BCL.83 16 PLIP interactions: 3 interactions with chain U, 4 interactions with chain R, 7 interactions with chain T, 2 interactions with chain S, Hydrophobic interactions: U:A.38, U:V.42, U:W.45, R:V.16, R:F.23, R:I.31, R:I.31, T:F.25, T:W.43, T:W.43, T:W.43, T:W.43, S:Y.24, S:F.49 pi-Stacking: T:H.32 Metal complexes: T:H.32 BCL.83: 19 residues within 4Å: Chain T: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain U: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Ligands: SPO.78, BCL.81, BCL.85 13 PLIP interactions: 10 interactions with chain U, 3 interactions with chain T, Hydrophobic interactions: U:F.31, U:I.32, U:A.35, U:V.36, U:V.42, U:W.48, U:W.48, U:W.48, T:I.31, T:I.31, T:F.41 pi-Cation interactions: U:H.39 Metal complexes: U:H.39 BCL.85: 20 residues within 4Å: Chain T: Q.20, F.23, I.31 Chain U: F.49 Chain V: G.21, L.24, F.25, A.28, H.32, W.43 Chain W: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: SPO.78, BCL.83, BCL.87 14 PLIP interactions: 4 interactions with chain T, 2 interactions with chain W, 7 interactions with chain V, 1 interactions with chain U, Hydrophobic interactions: T:F.23, T:F.23, T:I.31, T:I.31, W:V.42, W:W.45, V:L.24, V:A.28, V:W.43, V:W.43, V:W.43, V:W.43, U:F.49 Metal complexes: V:H.32 BCL.87: 12 residues within 4Å: Chain V: L.24, L.27, A.28, I.31, H.32 Chain W: F.31, I.32, A.35, V.36, H.39, V.42 Ligands: BCL.85 6 PLIP interactions: 5 interactions with chain W, 1 interactions with chain V, Hydrophobic interactions: W:I.32, W:A.35, W:V.36, W:V.42, V:I.31 Metal complexes: W:H.39

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.2: 31 residues within 4Å: Chain A: T.39, F.42, A.43, G.46, I.50, C.93, A.94, A.97, F.98, W.101, E.105, I.118, A.121, F.122, M.124, A.125, Y.149, G.150, I.151, H.154, A.238, V.242 Chain B: Y.209, A.212, L.213, A.216, M.217, W.251, M.255 Ligands: BCL.1, BCL.10 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.43, A:I.50, A:A.94, A:A.97, A:A.121, A:F.122, A:F.122, A:F.122, A:A.125, A:Y.149, A:Y.149, A:V.242, A:V.242, B:Y.209, B:A.212, B:A.216 BPH.16: 25 residues within 4Å: Chain A: F.182, A.185, W.186, A.189, M.190, L.220, M.221 Chain B: S.59, G.63, A.64, F.67, F.68, S.124, V.125, W.128, V.132, M.145, A.148, F.149, A.152, A.272, V.273, T.276 Ligands: BCL.14, BCL.15 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.64, B:F.67, B:F.68, B:A.148, B:F.149, B:F.149, B:T.276, A:F.182, A:A.185, A:A.189 pi-Stacking: A:W.186

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

U10.3: 24 residues within 4Å: Chain A: P.172, M.175, S.179, L.180, T.183, W.186, M.190, H.191, L.194, E.213, D.214, F.217, Y.223, S.224, V.225, G.226, T.227, I.230, L.233, W.264 Chain B: F.90, I.178 Ligands: BCL.14, LMT.22 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.180, A:T.183, A:W.186, A:M.190, A:L.194, A:F.217, A:F.217, A:Y.223, A:V.225, A:V.225, A:I.230, A:I.230, A:L.233, A:L.233, A:W.264, B:I.178 Hydrogen bonds: A:V.225, A:G.226 U10.4: 33 residues within 4Å: Chain A: L.22, V.37, F.41, F.42, V.78, Q.88, T.91, V.92, C.93, T.95, G.96, V.134, W.143 Chain D: V.16, A.19, Q.20, F.23, L.26, L.30, L.33, I.34 Chain F: V.18, G.21, V.22, F.25 Chain X: P.36, F.39, G.40, L.43, V.44 Ligands: PEE.6, LMT.37, BCL.40 25 PLIP interactions: 6 interactions with chain D, 3 interactions with chain X, 13 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: D:F.23, D:L.26, D:L.30, D:L.30, D:L.33, D:I.34, X:F.39, X:L.43, X:V.44, A:V.37, A:F.41, A:F.41, A:F.41, A:F.42, A:F.42, A:V.78, A:Q.88, A:T.91, A:T.95, A:V.134, A:W.143, A:W.143, F:V.22, F:F.25, F:F.25 U10.12: 8 residues within 4Å: Chain A: W.264, W.266, W.267 Chain B: M.86, L.89, F.90, F.91 Ligands: LMT.8 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.267, A:W.267, B:L.89, B:F.90 Hydrogen bonds: B:F.90 U10.18: 25 residues within 4Å: Chain A: F.30, V.32, G.36, I.40, W.101, R.104 Chain B: L.213, M.217, H.218, T.221, I.222, A.247, A.248, W.251, M.255, F.257, N.258, A.259, T.260, M.261, I.264, W.267 Ligands: BCL.10, LMT.11, PGV.34 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.213, B:M.217, B:W.251, B:F.257, B:A.259, B:I.264, B:I.264, B:W.267, B:W.267, A:F.30, A:F.30, A:F.30, A:V.32, A:I.40, A:W.101 Hydrogen bonds: B:A.259

8 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.5: 9 residues within 4Å: Chain A: W.60, N.61, P.62, Q.63 Chain J: L.33, S.37 Ligands: PGV.13, BCL.46, LMT.52 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.62, A:P.62 Hydrogen bonds: A:Q.63 PGV.13: 13 residues within 4Å: Chain A: Q.63, W.152 Chain B: P.199, L.203, A.206, H.300, Y.302 Chain C: I.17, W.18, W.21 Ligands: PGV.5, BCL.10, PGV.34 8 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:W.152, B:L.203, B:A.206, C:W.18, C:W.21, C:W.21 Hydrogen bonds: B:H.300 Salt bridges: B:H.300 PGV.24: 15 residues within 4Å: Chain A: N.200, P.201 Chain B: G.142, K.143, H.144, W.147, W.154, R.266, I.269, W.270, I.281 Chain C: F.23, Y.26, Y.30 Ligands: PGV.25 12 PLIP interactions: 2 interactions with chain C, 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:F.23, C:Y.26, B:W.147, B:W.154, B:W.154, B:W.154, B:I.269, B:I.281 Hydrogen bonds: B:K.143, A:N.200 Salt bridges: B:H.144, B:R.266 PGV.25: 10 residues within 4Å: Chain B: W.147, W.270, L.277, I.281 Chain C: A.16, S.19, F.20, F.23 Chain N: R.15 Ligands: PGV.24 9 PLIP interactions: 4 interactions with chain C, 1 interactions with chain N, 4 interactions with chain B Hydrophobic interactions: C:A.16, C:F.23, C:F.23, C:F.23, B:W.147, B:W.270, B:L.277, B:I.281 Hydrogen bonds: N:R.15 PGV.26: 16 residues within 4Å: Chain B: Y.51, G.53, I.54, A.55, V.58, I.123, I.126, T.134, R.135, Q.138 Chain R: R.15, A.19, V.22 Chain T: R.14, R.15 Ligands: LDA.31 12 PLIP interactions: 9 interactions with chain B, 1 interactions with chain T, 2 interactions with chain R Hydrophobic interactions: B:V.58, B:I.123, B:I.126, B:I.126, R:R.15 Hydrogen bonds: B:I.54, B:A.55, B:T.134, B:Q.138 Salt bridges: B:R.135, T:R.15, R:R.15 PGV.34: 20 residues within 4Å: Chain B: R.252, G.256, F.257, W.267, W.270, M.271 Chain C: L.24, I.28, L.31, Q.32, Y.40, L.42, N.52, G.54, P.55, F.56 Ligands: LMT.11, PGV.13, U10.18, BCL.46 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.24, C:I.28, C:I.28, C:I.28, C:L.31, C:F.56, B:F.257, B:F.257, B:W.267 Hydrogen bonds: C:N.52, B:R.252 Salt bridges: B:R.252 PGV.35: 12 residues within 4Å: Chain C: A.22, Y.26, Y.29, P.55, P.57 Chain J: F.11, D.12, R.15 Chain L: R.14, R.15, V.18 Ligands: BCL.46 6 PLIP interactions: 2 interactions with chain C, 3 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: C:Y.26, C:Y.29, L:V.18 Salt bridges: L:R.14, L:R.15 Hydrogen bonds: J:D.12 PGV.69: 12 residues within 4Å: Chain B: Y.133, W.162 Chain P: F.11, R.15, A.19, F.23 Chain R: V.18, V.22, F.25 Ligands: LDA.31, LDA.70, BCL.76 8 PLIP interactions: 2 interactions with chain B, 4 interactions with chain P, 2 interactions with chain R Hydrophobic interactions: B:W.162, P:F.23, R:V.22, R:F.25 Hydrogen bonds: B:Y.133, P:R.15, P:R.15 Salt bridges: P:R.15

1 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.6: 18 residues within 4Å: Chain A: L.17, F.42, G.96, C.99, S.100, A.102, L.103, V.106, R.110, P.119, V.120, S.123, I.126, F.127 Chain X: P.36 Ligands: U10.4, LDA.7, LMT.88 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain X Hydrophobic interactions: A:F.42, A:A.102, A:L.103, A:L.103, A:P.119, A:V.120, A:I.126, A:F.127, A:F.127, X:P.36 Salt bridges: A:R.110

11 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.7: 7 residues within 4Å: Chain A: F.116, V.120 Chain B: E.3, Q.5, R.227 Chain C: Y.243 Ligands: PEE.6 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.3, A:F.116, A:V.120, A:V.120 Hydrogen bonds: B:E.3 LDA.27: 4 residues within 4Å: Chain B: F.67, F.85 Ligands: BCL.14, SPO.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.67 LDA.29: 12 residues within 4Å: Chain A: M.221, G.222 Chain B: T.31, P.32, A.33, G.34, I.47, G.48, I.50 Ligands: BCL.14, LMT.28, LDA.30 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.47, B:I.50 LDA.30: 10 residues within 4Å: Chain B: T.31, I.50, L.52, G.56, T.57, L.60 Ligands: BCL.14, LMT.28, LDA.29, LMT.86 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.31, B:I.50, B:L.52, B:L.60 LDA.31: 6 residues within 4Å: Chain B: W.129, Y.133, W.147, L.150 Ligands: PGV.26, PGV.69 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.129, B:W.147, B:L.150 LDA.32: 9 residues within 4Å: Chain B: L.166, M.167, L.285, G.287, T.288 Chain C: M.1, L.12 Ligands: LMT.20, LDA.33 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.166, B:L.285, C:L.12 LDA.33: 5 residues within 4Å: Chain C: M.1 Ligands: LDA.32, LDA.61, LMT.67, LDA.68 No protein-ligand interaction detected (PLIP) LDA.42: 10 residues within 4Å: Chain A: V.27, V.32, I.40 Chain F: F.11, D.12, R.15, A.19 Chain H: R.14, V.18 Ligands: LMT.11 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:R.15, F:A.19, A:V.32, A:I.40 Hydrogen bonds: F:D.12 Salt bridges: F:D.12 LDA.61: 11 residues within 4Å: Chain C: M.1, V.4, F.6, L.15 Chain N: L.30, L.33, I.34, S.37, P.39 Ligands: LDA.33, LDA.68 6 PLIP interactions: 3 interactions with chain N, 3 interactions with chain C Hydrophobic interactions: N:L.30, N:L.33, N:I.34, C:F.6, C:F.6, C:L.15 LDA.68: 5 residues within 4Å: Chain P: L.36, N.42, T.45 Ligands: LDA.33, LDA.61 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:L.36 LDA.70: 6 residues within 4Å: Chain P: R.15, V.18, A.19, V.22, F.23 Ligands: PGV.69 2 PLIP interactions: 2 interactions with chain P Hydrophobic interactions: P:V.22, P:F.23

18 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.8: 4 residues within 4Å: Chain A: W.263, W.266 Ligands: LMT.9, U10.12 Ligand excluded by PLIP LMT.9: 8 residues within 4Å: Chain A: P.172, F.173, I.255, Y.256, F.257, W.260, W.263 Ligands: LMT.8 Ligand excluded by PLIP LMT.11: 15 residues within 4Å: Chain A: A.2, V.27, G.28, P.29, F.30 Chain B: M.255, G.256, F.257 Chain H: R.14, R.15, V.18 Ligands: U10.18, PGV.34, LDA.42, BCL.46 Ligand excluded by PLIP LMT.20: 8 residues within 4Å: Chain B: L.103, I.165, L.166, M.167, G.168 Ligands: LDA.32, LMT.67, LMT.74 Ligand excluded by PLIP LMT.21: 14 residues within 4Å: Chain B: L.103, A.104, L.105, F.161 Chain R: I.34, T.38, P.39 Chain T: L.33, L.36, S.37, N.42, T.45 Ligands: SPO.19, LMT.75 Ligand excluded by PLIP LMT.22: 11 residues within 4Å: Chain A: V.225, L.233 Chain B: F.8, N.9, Q.10, I.38, W.41, M.42 Chain C: G.147, R.148 Ligands: U10.3 Ligand excluded by PLIP LMT.23: 17 residues within 4Å: Chain B: A.65, F.68, T.69, V.72, W.73, Y.76, L.108, K.109, V.113, I.116, F.120 Chain V: L.26, V.29, L.30, L.33, I.34, S.37 Ligand excluded by PLIP LMT.28: 6 residues within 4Å: Chain B: G.34, M.35, L.36, I.47 Ligands: LDA.29, LDA.30 Ligand excluded by PLIP LMT.37: 11 residues within 4Å: Chain A: L.76, N.77, V.78 Chain D: L.33, L.36, N.42, L.44 Chain X: F.37, L.41 Ligands: U10.4, LMT.89 Ligand excluded by PLIP LMT.52: 12 residues within 4Å: Chain A: W.60 Chain H: L.30, I.34, T.38 Chain J: V.29, L.33, L.36, N.42, L.44, T.45 Ligands: PGV.5, MYR.47 Ligand excluded by PLIP LMT.57: 12 residues within 4Å: Chain C: G.8, D.9 Chain J: L.30, I.34, S.37, T.38 Chain L: V.29, L.33, L.36, S.37, N.42 Ligands: BCL.46 Ligand excluded by PLIP LMT.67: 12 residues within 4Å: Chain B: W.154, W.162, L.166, L.284 Chain P: S.37, T.38, P.39 Chain R: N.42, T.45 Ligands: LMT.20, LDA.33, LMT.74 Ligand excluded by PLIP LMT.74: 11 residues within 4Å: Chain B: L.103, I.165, G.168 Chain R: L.33, L.36, S.37, P.39, N.42 Ligands: LMT.20, LMT.67, LMT.75 Ligand excluded by PLIP LMT.75: 9 residues within 4Å: Chain B: E.100, Y.101, G.102, L.103, A.104 Chain R: L.33, S.37 Ligands: LMT.21, LMT.74 Ligand excluded by PLIP LMT.84: 11 residues within 4Å: Chain B: L.105, A.106, P.107, L.108, I.116 Chain T: I.34, S.37 Chain V: L.36, S.37, N.42, T.45 Ligand excluded by PLIP LMT.86: 10 residues within 4Å: Chain B: Y.28, R.30, T.31, P.32, L.52, L.60 Chain V: D.12, R.14, R.15 Ligands: LDA.30 Ligand excluded by PLIP LMT.88: 14 residues within 4Å: Chain A: T.16, L.17, I.18, F.34, F.35, L.103 Chain C: G.248 Chain D: R.15, V.22 Chain X: S.2, Y.28, L.32, P.36 Ligands: PEE.6 Ligand excluded by PLIP LMT.89: 12 residues within 4Å: Chain A: L.76 Chain D: H.32, L.33, W.43, L.44 Chain X: F.37, L.41, L.45, Y.48, L.52 Ligands: BCL.36, LMT.37 Ligand excluded by PLIP

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

FE.17: 5 residues within 4Å: Chain A: H.191, H.231 Chain B: H.218, E.233, H.265 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.191, A:H.231, B:H.218, B:E.233, B:H.265

18 x SPO: SPHEROIDENE(Non-covalent)

SPO.19: 27 residues within 4Å: Chain B: W.66, F.67, F.68, I.70, G.71, Y.74, W.75, F.85, L.89, Q.115, S.118, M.121, A.122, W.156, S.157, G.160, F.161, W.170, V.174, Y.176, G.177, I.178, H.181 Chain T: L.33 Ligands: BCL.14, LMT.21, LDA.27 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain T Hydrophobic interactions: B:W.66, B:F.67, B:F.67, B:F.67, B:F.68, B:I.70, B:I.70, B:Y.74, B:L.89, B:Q.115, B:A.122, B:W.156, B:W.170, B:V.174, B:V.174, B:Y.176, B:I.178, T:L.33 SPO.39: 25 residues within 4Å: Chain D: Q.20, F.23, L.24, L.27, L.30, I.34 Chain E: V.23, Y.24, S.26, G.27, L.28, F.31 Chain F: F.25, A.28, H.32, L.33 Chain X: K.15, G.19, I.20, I.22, M.26 Ligands: BCL.36, BCL.38, BCL.40, SPO.44 15 PLIP interactions: 6 interactions with chain D, 2 interactions with chain X, 2 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: D:F.23, D:F.23, D:L.24, D:L.27, D:L.30, D:I.34, X:I.20, X:I.22, F:F.25, F:A.28, E:V.23, E:V.23, E:L.28, E:L.28, E:F.31 SPO.41: 26 residues within 4Å: Chain D: F.4, K.6, I.7, V.10 Chain E: L.7 Chain F: F.17, Q.20, F.23, L.24, L.27, I.31, I.34 Chain G: L.20, V.23, Y.24, G.27, L.28, F.31 Chain H: F.25, A.28, V.29, H.32, L.33 Ligands: SPO.44, BCL.45, BCL.48 24 PLIP interactions: 4 interactions with chain H, 4 interactions with chain D, 9 interactions with chain G, 6 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: H:F.25, H:A.28, H:V.29, H:H.32, D:F.4, D:K.6, D:K.6, D:I.7, G:L.20, G:L.20, G:L.20, G:V.23, G:V.23, G:Y.24, G:L.28, G:L.28, G:F.31, F:F.23, F:F.23, F:L.24, F:L.27, F:L.27, F:I.31, E:L.7 SPO.43: 28 residues within 4Å: Chain F: F.4, K.6, I.7, V.10, F.11 Chain G: L.7 Chain H: F.17, Q.20, F.23, L.24, L.27, I.34 Chain I: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain J: F.25, A.28, H.32, L.33, L.36 Ligands: BCL.48, SPO.49, BCL.50, BCL.53 20 PLIP interactions: 6 interactions with chain H, 5 interactions with chain F, 5 interactions with chain I, 1 interactions with chain G, 3 interactions with chain J Hydrophobic interactions: H:F.17, H:F.23, H:F.23, H:L.24, H:L.27, H:I.34, F:F.4, F:K.6, F:I.7, F:I.7, F:F.11, I:L.20, I:L.20, I:V.23, I:Y.24, I:F.31, G:L.7, J:A.28, J:H.32, J:L.36 SPO.44: 11 residues within 4Å: Chain E: M.43, F.49 Chain F: Q.20 Chain G: V.34, A.38, A.41, W.45 Ligands: BCL.38, SPO.39, BCL.40, SPO.41 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain E Hydrophobic interactions: G:V.34, G:A.41, G:W.45, E:F.49, E:F.49 SPO.49: 13 residues within 4Å: Chain G: M.43, F.49 Chain H: F.17, Q.20, G.21 Chain I: F.31, V.34, A.38, A.41, W.45 Ligands: SPO.43, BCL.45, BCL.48 7 PLIP interactions: 1 interactions with chain H, 3 interactions with chain I, 3 interactions with chain G Hydrophobic interactions: H:F.17, I:F.31, I:V.34, I:A.41, G:F.49, G:F.49, G:F.49 SPO.51: 12 residues within 4Å: Chain I: F.49 Chain J: F.17, Q.20 Chain K: F.31, V.34, A.38, A.41, V.42, W.45 Ligands: BCL.50, BCL.53, SPO.54 7 PLIP interactions: 2 interactions with chain I, 4 interactions with chain K, 1 interactions with chain J Hydrophobic interactions: I:F.49, I:F.49, K:F.31, K:V.34, K:V.42, K:W.45, J:F.17 SPO.54: 25 residues within 4Å: Chain H: F.4, K.6, I.7, V.10 Chain J: F.17, Q.20, F.23, L.24, L.27, L.30, I.34 Chain K: L.20, V.23, Y.24, G.27, L.28, F.31 Chain L: F.25, A.28, V.29, H.32, L.33 Ligands: SPO.51, BCL.56, BCL.58 22 PLIP interactions: 3 interactions with chain L, 6 interactions with chain K, 9 interactions with chain J, 4 interactions with chain H Hydrophobic interactions: L:F.25, L:A.28, L:H.32, K:L.20, K:L.20, K:V.23, K:V.23, K:Y.24, K:F.31, J:F.17, J:F.17, J:F.23, J:F.23, J:L.24, J:L.24, J:L.27, J:L.30, J:I.34, H:F.4, H:K.6, H:K.6, H:I.7 SPO.55: 25 residues within 4Å: Chain J: F.4, K.6, I.7, V.10 Chain K: L.7 Chain L: F.17, Q.20, F.23, L.24, L.27, I.34 Chain M: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain N: F.25, A.28, H.32, L.33 Ligands: SPO.59, BCL.60, BCL.62 22 PLIP interactions: 8 interactions with chain L, 3 interactions with chain N, 5 interactions with chain M, 6 interactions with chain J Hydrophobic interactions: L:F.17, L:F.17, L:F.23, L:F.23, L:L.24, L:L.24, L:L.27, L:I.34, N:F.25, N:A.28, N:H.32, M:E.19, M:V.23, M:L.28, M:L.28, M:F.31, J:F.4, J:K.6, J:K.6, J:I.7, J:I.7, J:V.10 SPO.59: 12 residues within 4Å: Chain K: F.49 Chain L: F.17, Q.20 Chain M: F.31, V.34, A.38, A.41, V.42, W.45 Ligands: SPO.55, BCL.56, BCL.58 8 PLIP interactions: 3 interactions with chain M, 4 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: M:F.31, M:V.34, M:V.42, K:F.49, K:F.49, K:F.49, K:F.49, L:F.17 SPO.63: 24 residues within 4Å: Chain L: F.4, K.6, I.7, V.10 Chain M: L.7 Chain N: F.17, Q.20, F.23, L.24, L.27, L.30 Chain O: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain P: F.25, H.32, L.33 Ligands: SPO.65, BCL.66, BCL.71 22 PLIP interactions: 8 interactions with chain O, 5 interactions with chain L, 2 interactions with chain P, 6 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: O:E.19, O:L.20, O:V.23, O:V.23, O:V.23, O:L.28, O:L.28, O:F.31, L:F.4, L:K.6, L:K.6, L:I.7, L:V.10, P:F.25, P:H.32, N:F.17, N:F.23, N:F.23, N:L.24, N:L.27, N:L.30, M:L.7 SPO.64: 26 residues within 4Å: Chain N: F.4, K.6, I.7, V.10 Chain O: L.7 Chain P: F.17, Q.20, F.23, L.24, L.27, L.30, I.31 Chain Q: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain R: F.25, V.29, H.32, L.33 Ligands: SPO.72, BCL.73, BCL.76 20 PLIP interactions: 3 interactions with chain N, 6 interactions with chain Q, 7 interactions with chain P, 3 interactions with chain R, 1 interactions with chain O Hydrophobic interactions: N:F.4, N:K.6, N:I.7, Q:L.20, Q:V.23, Q:V.23, Q:V.23, Q:L.28, Q:F.31, P:F.17, P:F.23, P:F.23, P:L.24, P:L.27, P:L.30, P:I.31, R:F.25, R:V.29, R:H.32, O:L.7 SPO.65: 12 residues within 4Å: Chain M: F.49 Chain N: F.17, G.21, K.50 Chain O: F.31, V.34, A.38, A.41, W.45 Ligands: BCL.60, BCL.62, SPO.63 11 PLIP interactions: 5 interactions with chain O, 2 interactions with chain N, 4 interactions with chain M Hydrophobic interactions: O:F.31, O:F.31, O:V.34, O:A.41, O:W.45, N:F.17, M:F.49, M:F.49, M:F.49, M:F.49 Hydrogen bonds: N:K.50 SPO.72: 13 residues within 4Å: Chain O: F.49 Chain P: F.17, Q.20, G.21, K.50 Chain Q: V.34, A.38, A.41, V.42, W.45 Ligands: SPO.64, BCL.66, BCL.71 5 PLIP interactions: 3 interactions with chain Q, 2 interactions with chain O Hydrophobic interactions: Q:V.34, Q:A.41, Q:V.42, O:F.49, O:F.49 SPO.77: 28 residues within 4Å: Chain P: F.4, K.6, I.7, V.10 Chain Q: L.7 Chain R: F.17, Q.20, F.23, L.24, L.27, L.30, I.31 Chain S: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain T: F.25, A.28, V.29, H.32, L.33 Ligands: BCL.76, SPO.79, BCL.80, BCL.81 25 PLIP interactions: 6 interactions with chain R, 4 interactions with chain T, 8 interactions with chain S, 2 interactions with chain Q, 5 interactions with chain P Hydrophobic interactions: R:F.17, R:F.23, R:F.23, R:L.24, R:L.27, R:I.31, T:F.25, T:A.28, T:V.29, T:H.32, S:L.20, S:L.20, S:V.23, S:V.23, S:Y.24, S:L.28, S:L.28, S:F.31, Q:L.7, Q:L.7, P:F.4, P:K.6, P:I.7, P:I.7, P:V.10 SPO.78: 24 residues within 4Å: Chain R: F.4, K.6, I.7, V.10 Chain T: Q.20, F.23, L.24, L.27, L.30, I.31 Chain U: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain V: F.25, V.29, H.32, L.33 Ligands: SPO.82, BCL.83, BCL.85 18 PLIP interactions: 7 interactions with chain T, 5 interactions with chain R, 5 interactions with chain U, 1 interactions with chain V Hydrophobic interactions: T:F.23, T:F.23, T:L.24, T:L.27, T:L.27, T:L.30, T:I.31, R:F.4, R:F.4, R:K.6, R:I.7, R:I.7, U:E.19, U:L.20, U:V.23, U:Y.24, U:F.31, V:F.25 SPO.79: 12 residues within 4Å: Chain Q: F.49 Chain R: F.17, Q.20, K.50 Chain S: F.31, V.34, A.38, A.41, W.45 Ligands: BCL.73, BCL.76, SPO.77 8 PLIP interactions: 4 interactions with chain S, 2 interactions with chain R, 2 interactions with chain Q Hydrophobic interactions: S:F.31, S:V.34, S:A.41, S:W.45, R:F.17, Q:F.49, Q:F.49 Hydrogen bonds: R:K.50 SPO.82: 10 residues within 4Å: Chain S: F.49 Chain T: F.17, K.50 Chain U: V.34, A.38, A.41, W.45 Ligands: SPO.78, BCL.80, BCL.81 7 PLIP interactions: 2 interactions with chain T, 2 interactions with chain S, 3 interactions with chain U Hydrophobic interactions: T:F.17, S:F.49, S:F.49, U:V.34, U:A.41, U:W.45 Hydrogen bonds: T:K.50

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.47: 10 residues within 4Å: Chain H: R.15, A.19, V.22, F.23, L.26, L.27, L.30 Chain J: F.25 Ligands: BCL.46, LMT.52 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain J Hydrophobic interactions: H:V.22, H:F.23, H:L.26, H:L.30, J:F.25, J:F.25 Salt bridges: H:R.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tani, K. et al., Rhodobacter capsulatus forms a compact crescent-shaped LH1-RC photocomplex. Nat Commun (2023)

Release Date

2023-02-22

Peptides

Reaction center protein L chain: A
Reaction center protein M chain: B
Photosynthetic reaction center H subunit: C
Light-harvesting protein B-870 alpha chain: DFHJLNPRTV
Light-harvesting protein B-870 beta chain: EGIKMOQSUW
Photosynthetic reaction center PufX protein: X

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
V

V
Y

E
B

G
E

I
G

K
J

M
N

O
P

Q
R

S
T

U
W

W
Z

X
X

Membrane

We predict this structure to be a membrane protein.
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Reaction center protein L chain

Reaction center protein M chain

Photosynthetic reaction center H subunit

Light-harvesting protein B-870 alpha chain

Light-harvesting protein B-870 beta chain

Photosynthetic reaction center PufX protein

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