SMTL ID : 7ddq.1

Structure of RC-LH1-PufX from Rhodobacter veldkampii

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-15-15-1-1-1-1-mer

Ligands

34 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 21 residues within 4Å: Chain A: G.21, V.22, L.24, F.25, A.28, H.32, L.35, W.43 Chain F: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain V: Q.20, F.23 Ligands: SPO.2, BCL.3, SPO.9, BCL.11 14 PLIP interactions: 2 interactions with chain V, 9 interactions with chain A, 3 interactions with chain F, Hydrophobic interactions: V:F.23, V:F.23, A:L.24, A:F.25, A:A.28, A:L.35, A:W.43, A:W.43, A:W.43, A:W.43, F:F.30, F:A.37, F:W.44 Metal complexes: A:H.32 BCL.3: 19 residues within 4Å: Chain A: W.43, L.44 Chain B: F.30, I.31, I.35, H.38, V.41, W.47, L.48 Chain V: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.1, SPO.2, BCL.30 12 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B, 3 interactions with chain V, Hydrophobic interactions: A:L.44, B:F.30, B:I.35, B:V.41, B:W.47, B:W.47, B:W.47, B:L.48, V:I.31, V:I.31, V:F.41 Metal complexes: B:H.38 BCL.4: 21 residues within 4Å: Chain C: G.21, L.24, F.25, A.28, H.32, W.43 Chain D: Y.23 Chain R: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain T: Q.20, F.23, I.31 Ligands: SPO.5, BCL.6, BCL.7, SPO.27 8 PLIP interactions: 5 interactions with chain C, 1 interactions with chain R, 2 interactions with chain T, Hydrophobic interactions: C:W.43, C:W.43, C:W.43, C:W.43, R:W.44, T:Q.20, T:I.31 Metal complexes: C:H.32 BCL.6: 20 residues within 4Å: Chain C: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain Q: W.43, L.44 Chain R: F.30, A.34, I.35, H.38, L.39, V.41, F.42, W.47 Ligands: BCL.4, SPO.5, BCL.24 16 PLIP interactions: 12 interactions with chain R, 3 interactions with chain C, 1 interactions with chain Q, Hydrophobic interactions: R:F.30, R:A.34, R:I.35, R:L.39, R:V.41, R:F.42, R:F.42, R:F.42, R:W.47, R:W.47, R:W.47, C:I.31, C:I.31, C:F.41, Q:L.44 Metal complexes: R:H.38 BCL.7: 20 residues within 4Å: Chain C: W.43, L.44 Chain D: F.30, A.34, I.35, H.38, L.39, V.41, W.47, L.48 Chain T: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.4, SPO.27, BCL.28 16 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C, 4 interactions with chain T, Hydrophobic interactions: D:F.30, D:A.34, D:I.35, D:H.38, D:L.39, D:L.39, D:V.41, D:W.47, D:W.47, D:W.47, C:L.44, T:I.31, T:I.31, T:L.35, T:F.41 Metal complexes: D:H.38 BCL.8: 20 residues within 4Å: Chain A: Q.20, F.23 Chain E: G.21, L.24, F.25, A.28, H.32, W.43 Chain F: M.27 Chain U: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Ligands: SPO.9, SPO.10, BCL.11, BCL.29 12 PLIP interactions: 3 interactions with chain U, 1 interactions with chain A, 8 interactions with chain E, Hydrophobic interactions: U:F.30, U:A.37, U:W.44, A:F.23, E:L.24, E:L.24, E:F.25, E:W.43, E:W.43, E:W.43, E:W.43 Metal complexes: E:H.32 BCL.11: 19 residues within 4Å: Chain A: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain E: W.43 Chain F: F.30, A.34, I.35, H.38, L.39, V.41, F.42, W.47 Ligands: BCL.1, BCL.8, SPO.9 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain F, Hydrophobic interactions: A:I.31, A:I.31, A:F.41, F:F.30, F:A.34, F:I.35, F:H.38, F:L.39, F:V.41, F:F.42, F:F.42, F:W.47, F:W.47, F:W.47 Metal complexes: F:H.38 BCL.12: 17 residues within 4Å: Chain G: A.28, H.32, L.35, W.43 Chain L: G.26, L.29, F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain S: A.20, G.24 Ligands: BCL.19, SPO.26 14 PLIP interactions: 7 interactions with chain G, 7 interactions with chain L, Hydrophobic interactions: G:A.28, G:L.35, G:W.43, G:W.43, G:W.43, G:W.43, L:L.29, L:F.30, L:F.30, L:V.33, L:V.33, L:A.37, L:W.44 Metal complexes: G:H.32 BCL.14: 24 residues within 4Å: Chain 6: I.7, Q.20, F.23, I.31, M.34 Chain I: G.21, L.24, F.25, A.28, H.32, W.43 Chain J: H.20, Y.23, M.27 Chain P: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Ligands: SPO.15, BCL.16, BCL.23 15 PLIP interactions: 4 interactions with chain 6, 1 interactions with chain J, 3 interactions with chain P, 7 interactions with chain I, Hydrophobic interactions: 6:I.7, 6:F.23, 6:I.31, 6:I.31, J:Y.23, P:F.30, P:A.37, P:W.44, I:L.24, I:F.25, I:W.43, I:W.43, I:W.43, I:W.43 Metal complexes: I:H.32 BCL.16: 18 residues within 4Å: Chain 6: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain I: W.43 Chain J: F.30, A.34, I.35, H.38, L.39, V.41, W.47 Ligands: BCL.14, SPO.15, BCL.60 15 PLIP interactions: 4 interactions with chain 6, 11 interactions with chain J, Hydrophobic interactions: 6:I.31, 6:I.31, 6:L.35, 6:F.41, J:F.30, J:A.34, J:I.35, J:H.38, J:L.39, J:V.41, J:W.47, J:W.47, J:W.47, J:W.47 Metal complexes: J:H.38 BCL.17: 28 residues within 4Å: Chain 1: F.34, V.37, T.38 Chain 7: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain G: V.16, A.19, Q.20, V.22, F.23, I.31, M.34 Chain K: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Ligands: U10.13, BCL.18, BCL.19, SPO.26 19 PLIP interactions: 2 interactions with chain 1, 3 interactions with chain 7, 5 interactions with chain G, 9 interactions with chain K, Hydrophobic interactions: 1:V.37, 1:T.38, 7:A.37, 7:V.41, 7:W.44, G:V.16, G:V.22, G:F.23, G:I.31, G:I.31, K:L.24, K:L.24, K:F.25, K:A.28, K:L.35, K:W.43, K:W.43, K:W.43, K:W.43 BCL.18: 19 residues within 4Å: Chain 6: W.43 Chain 7: F.30, I.31, A.34, I.35, H.38, V.41, W.47, L.48 Chain K: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.17, BCL.60, SPO.62 13 PLIP interactions: 9 interactions with chain 7, 4 interactions with chain K, Hydrophobic interactions: 7:F.30, 7:A.34, 7:I.35, 7:V.41, 7:W.47, 7:W.47, 7:W.47, 7:L.48, K:I.31, K:I.31, K:L.35, K:F.41 Metal complexes: 7:H.38 BCL.19: 18 residues within 4Å: Chain G: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain K: W.43 Chain L: F.30, I.31, A.34, H.38, V.41, F.42, W.47 Ligands: BCL.12, BCL.17, SPO.26 13 PLIP interactions: 10 interactions with chain L, 3 interactions with chain G, Hydrophobic interactions: L:F.30, L:I.31, L:H.38, L:V.41, L:F.42, L:F.42, L:W.47, L:W.47, L:W.47, G:I.31, G:I.31, G:F.41 Metal complexes: L:H.38 BCL.20: 21 residues within 4Å: Chain M: G.21, L.24, F.25, A.28, H.32, W.43 Chain W: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain Z: Q.20, F.23, I.31, M.34 Ligands: SPO.21, BCL.31, SPO.34, BCL.36 11 PLIP interactions: 3 interactions with chain Z, 3 interactions with chain W, 5 interactions with chain M, Hydrophobic interactions: Z:F.23, Z:I.31, Z:I.31, W:A.37, W:V.41, W:W.44, M:W.43, M:W.43, M:W.43, M:W.43 Metal complexes: M:H.32 BCL.23: 19 residues within 4Å: Chain I: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain O: W.43 Chain P: F.30, I.31, A.34, H.38, L.39, V.41, F.42, W.47 Ligands: BCL.14, SPO.22, BCL.57 15 PLIP interactions: 12 interactions with chain P, 3 interactions with chain I, Hydrophobic interactions: P:F.30, P:I.31, P:A.34, P:L.39, P:V.41, P:F.42, P:F.42, P:W.47, P:W.47, P:W.47, P:W.47, I:I.31, I:L.35, I:F.41 Metal complexes: P:H.38 BCL.24: 21 residues within 4Å: Chain C: I.7, Q.20, F.23, M.34 Chain H: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain Q: G.21, L.24, F.25, A.28, H.32, W.43 Chain R: Y.23 Ligands: SPO.5, BCL.6, BCL.25 15 PLIP interactions: 3 interactions with chain C, 5 interactions with chain H, 6 interactions with chain Q, 1 interactions with chain R, Hydrophobic interactions: C:I.7, C:Q.20, C:F.23, H:F.30, H:A.37, H:V.41, H:V.41, H:W.44, Q:F.25, Q:W.43, Q:W.43, Q:W.43, Q:W.43, R:Y.23 Metal complexes: Q:H.32 BCL.25: 16 residues within 4Å: Chain H: F.30, I.31, A.34, I.35, H.38, L.39, V.41, W.47 Chain Q: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.24 13 PLIP interactions: 9 interactions with chain H, 4 interactions with chain Q, Hydrophobic interactions: H:F.30, H:I.31, H:A.34, H:I.35, H:H.38, H:L.39, H:V.41, H:W.47, Q:I.31, Q:I.31, Q:L.35, Q:F.41 Metal complexes: H:H.38 BCL.28: 20 residues within 4Å: Chain D: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain E: I.31, M.34 Chain T: G.21, L.24, F.25, A.28, H.32, W.43 Chain U: L.48 Ligands: BCL.7, SPO.10, SPO.27, BCL.29 13 PLIP interactions: 2 interactions with chain E, 7 interactions with chain T, 3 interactions with chain D, 1 interactions with chain U, Hydrophobic interactions: E:I.31, E:I.31, T:L.24, T:L.24, T:W.43, T:W.43, T:W.43, T:W.43, D:F.30, D:A.37, D:W.44, U:L.48 Metal complexes: T:H.32 BCL.29: 22 residues within 4Å: Chain E: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain T: W.43, L.44 Chain U: F.30, I.31, A.34, I.35, H.38, L.39, V.41, F.42, W.47, L.48 Ligands: BCL.8, SPO.10, BCL.28 19 PLIP interactions: 14 interactions with chain U, 4 interactions with chain E, 1 interactions with chain T, Hydrophobic interactions: U:F.30, U:I.31, U:A.34, U:I.35, U:H.38, U:L.39, U:V.41, U:F.42, U:F.42, U:F.42, U:W.47, U:W.47, U:W.47, E:I.31, E:I.31, E:L.35, E:F.41, T:L.44 Metal complexes: U:H.38 BCL.30: 24 residues within 4Å: Chain B: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain M: I.7, Q.20, F.23, I.31 Chain V: G.21, L.24, F.25, A.28, H.32, W.43 Chain W: H.20, Y.23, M.27 Ligands: SPO.2, BCL.3, SPO.21, BCL.31 13 PLIP interactions: 3 interactions with chain M, 3 interactions with chain B, 6 interactions with chain V, 1 interactions with chain W, Hydrophobic interactions: M:I.7, M:F.23, M:I.31, B:A.37, B:V.41, B:W.44, V:L.24, V:W.43, V:W.43, V:W.43, V:W.43, W:Y.23 Metal complexes: V:H.32 BCL.31: 17 residues within 4Å: Chain M: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain W: F.30, A.34, I.35, H.38, V.41, W.47, L.48 Ligands: BCL.20, SPO.21, BCL.30 12 PLIP interactions: 9 interactions with chain W, 3 interactions with chain M, Hydrophobic interactions: W:F.30, W:A.34, W:I.35, W:V.41, W:W.47, W:W.47, W:W.47, W:L.48, M:I.31, M:I.31, M:F.41 Metal complexes: W:H.38 BCL.32: 21 residues within 4Å: Chain 0: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain 4: F.23, I.31 Chain X: G.21, L.24, F.25, A.28, H.32, W.43 Chain Y: Y.23, L.48 Ligands: BCL.33, BCL.37, SPO.38, SPO.56 13 PLIP interactions: 2 interactions with chain 0, 3 interactions with chain 4, 1 interactions with chain Y, 7 interactions with chain X, Hydrophobic interactions: 0:A.37, 0:W.44, 4:F.23, 4:F.23, 4:I.31, Y:L.48, X:L.24, X:F.25, X:W.43, X:W.43, X:W.43, X:W.43 Metal complexes: X:H.32 BCL.33: 19 residues within 4Å: Chain 4: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain Y: F.30, A.34, I.35, H.38, L.39, V.41, F.42, W.47, L.48 Ligands: BCL.32, BCL.55, SPO.56 14 PLIP interactions: 4 interactions with chain 4, 10 interactions with chain Y, Hydrophobic interactions: 4:I.31, 4:I.31, 4:L.35, 4:F.41, Y:F.30, Y:A.34, Y:I.35, Y:L.39, Y:V.41, Y:F.42, Y:W.47, Y:W.47, Y:W.47 Metal complexes: Y:H.38 BCL.35: 18 residues within 4Å: Chain 0: H.20, M.27 Chain N: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain Z: G.21, L.24, F.25, A.28, H.32, W.43 Ligands: BCL.36, BCL.37, SPO.38 9 PLIP interactions: 6 interactions with chain Z, 3 interactions with chain N, Hydrophobic interactions: Z:L.24, Z:W.43, Z:W.43, Z:W.43, Z:W.43, N:F.30, N:A.37, N:W.44 Metal complexes: Z:H.32 BCL.36: 18 residues within 4Å: Chain N: F.30, A.34, I.35, H.38, L.39, V.41, F.42, W.47 Chain Z: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.20, SPO.34, BCL.35 15 PLIP interactions: 13 interactions with chain N, 2 interactions with chain Z, Hydrophobic interactions: N:F.30, N:A.34, N:I.35, N:L.39, N:V.41, N:F.42, N:F.42, N:F.42, N:W.47, N:W.47, N:W.47, N:W.47, Z:I.31, Z:F.41 Metal complexes: N:H.38 BCL.37: 20 residues within 4Å: Chain 0: F.30, A.34, I.35, H.38, V.41, F.42, W.47, L.48 Chain X: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain Z: W.43, L.44 Ligands: BCL.32, BCL.35, SPO.38 15 PLIP interactions: 11 interactions with chain 0, 3 interactions with chain X, 1 interactions with chain Z, Hydrophobic interactions: 0:F.30, 0:A.34, 0:I.35, 0:V.41, 0:F.42, 0:F.42, 0:W.47, 0:W.47, 0:W.47, 0:L.48, X:I.31, X:I.31, X:F.41, Z:L.44 Metal complexes: 0:H.38 BCL.39: 30 residues within 4Å: Chain 1: F.98, F.122, A.125, I.126, A.128, Y.129, L.132, W.157, V.158, N.159, V.161, G.162, Y.163, N.167, F.168, H.169, H.174, G.177, I.178, F.181, S.245, A.246, I.249 Chain 2: T.187, Y.211 Ligands: BPH.40, BCL.45, BCL.46, U10.49, BCL.51 14 PLIP interactions: 13 interactions with chain 1, 1 interactions with chain 2, Hydrophobic interactions: 1:F.122, 1:A.128, 1:L.132, 1:V.161, 1:Y.163, 1:F.168, 1:F.168, 1:I.178, 1:F.181, 1:F.181, 1:F.181, 1:I.249, 2:Y.211 Metal complexes: 1:H.174 BCL.45: 21 residues within 4Å: Chain 1: I.50, Y.129, L.132, F.147, V.151, F.152, H.154, L.155 Chain 2: F.198, G.204, I.207, A.208, Y.211, G.212, M.215, F.273 Ligands: BCL.39, BPH.40, BCL.46, U10.49, 3PE.54 13 PLIP interactions: 7 interactions with chain 1, 6 interactions with chain 2, Hydrophobic interactions: 1:I.50, 1:Y.129, 1:L.132, 1:F.147, 1:F.147, 1:L.155, 2:F.198, 2:I.207, 2:I.207, 2:A.208, 2:F.273 Metal complexes: 1:H.154 pi-Stacking: 2:Y.211 BCL.46: 28 residues within 4Å: Chain 1: V.158, Y.163, H.169, F.182 Chain 2: V.127, A.154, L.157, M.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, T.277, P.278, G.281, I.285 Ligands: BCL.39, BCL.45, BPH.47, BCL.51 15 PLIP interactions: 15 interactions with chain 2, Hydrophobic interactions: 2:V.127, 2:A.154, 2:L.157, 2:M.158, 2:T.187, 2:F.190, 2:L.197, 2:F.198, 2:F.198, 2:I.207, 2:L.210, 2:Y.211, 2:T.277 Hydrogen bonds: 2:S.206 Metal complexes: 2:H.203 BCL.51: 22 residues within 4Å: Chain 1: H.169, M.175, I.178, S.179, F.182, T.183 Chain 2: F.68, L.90, F.91, M.158, L.161, I.180, H.183, L.184, W.186, T.187 Ligands: BCL.39, U10.41, U10.42, BCL.46, BPH.47, SPO.50 10 PLIP interactions: 6 interactions with chain 2, 4 interactions with chain 1, Hydrophobic interactions: 2:F.68, 2:L.90, 2:F.91, 2:L.161, 2:L.184, 2:W.186, 1:I.178, 1:I.178, 1:T.183 pi-Stacking: 1:F.182 BCL.55: 22 residues within 4Å: Chain 4: G.21, L.24, F.25, A.28, H.32, W.43 Chain 5: Y.23 Chain O: Q.20, F.23, I.31, M.34 Chain Y: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Ligands: BCL.33, SPO.56, SPO.58, BCL.59 12 PLIP interactions: 6 interactions with chain 4, 4 interactions with chain O, 2 interactions with chain Y, Hydrophobic interactions: 4:L.24, 4:W.43, 4:W.43, 4:W.43, 4:W.43, O:Q.20, O:F.23, O:F.23, O:I.31, Y:A.37, Y:W.44 Metal complexes: 4:H.32 BCL.57: 24 residues within 4Å: Chain 5: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain I: I.7, Q.20, F.23, I.31 Chain O: G.21, L.24, F.25, A.28, H.32, W.43 Chain P: H.20, Y.23, L.48 Ligands: SPO.22, BCL.23, SPO.58, BCL.59 17 PLIP interactions: 7 interactions with chain O, 3 interactions with chain 5, 5 interactions with chain I, 2 interactions with chain P, Hydrophobic interactions: O:L.24, O:F.25, O:W.43, O:W.43, O:W.43, O:W.43, 5:F.30, 5:A.37, 5:W.44, I:I.7, I:Q.20, I:F.23, I:I.31, I:I.31, P:Y.23, P:L.48 Metal complexes: O:H.32 BCL.59: 21 residues within 4Å: Chain 4: W.43 Chain 5: F.30, I.31, A.34, I.35, H.38, L.39, V.41, F.42, W.47, L.48 Chain O: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.55, BCL.57, SPO.58 13 PLIP interactions: 9 interactions with chain 5, 4 interactions with chain O, Hydrophobic interactions: 5:F.30, 5:I.35, 5:H.38, 5:V.41, 5:F.42, 5:W.47, 5:W.47, 5:W.47, O:I.31, O:I.31, O:L.35, O:F.41 Metal complexes: 5:H.38 BCL.60: 19 residues within 4Å: Chain 6: G.21, L.24, F.25, A.28, H.32, W.43 Chain J: F.30, V.33, A.34, A.37, H.38, V.41, W.44 Chain K: F.23, I.31 Ligands: BCL.16, BCL.18, 3PE.61, SPO.62 12 PLIP interactions: 6 interactions with chain 6, 3 interactions with chain J, 3 interactions with chain K, Hydrophobic interactions: 6:L.24, 6:F.25, 6:W.43, 6:W.43, 6:W.43, J:V.33, J:A.37, J:W.44, K:F.23, K:I.31, K:I.31 Metal complexes: 6:H.32

15 x SPO: SPHEROIDENE(Non-covalent)

SPO.2: 19 residues within 4Å: Chain A: F.25, A.28, H.32, L.36, L.44 Chain B: Y.23, G.26, M.27, F.30 Chain M: F.4 Chain V: F.23, L.24, L.27, I.31, M.34, L.35 Ligands: BCL.1, BCL.3, BCL.30 13 PLIP interactions: 4 interactions with chain V, 5 interactions with chain A, 1 interactions with chain M, 3 interactions with chain B Hydrophobic interactions: V:F.23, V:L.24, V:I.31, V:M.34, A:F.25, A:A.28, A:H.32, A:L.36, A:L.44, M:F.4, B:Y.23, B:Y.23, B:F.30 SPO.5: 18 residues within 4Å: Chain C: F.17, F.23, L.24, L.27, M.34 Chain Q: F.25, H.32, L.33, L.36 Chain R: V.22, Y.23, G.26, M.27, F.30 Chain T: I.7 Ligands: BCL.4, BCL.6, BCL.24 12 PLIP interactions: 4 interactions with chain R, 5 interactions with chain C, 2 interactions with chain Q, 1 interactions with chain T Hydrophobic interactions: R:V.22, R:Y.23, R:M.27, R:F.30, C:F.23, C:F.23, C:L.24, C:L.27, C:L.27, Q:L.33, Q:L.36, T:I.7 SPO.9: 18 residues within 4Å: Chain A: Q.20, F.23, L.24, L.27, M.34 Chain E: F.25, H.32, L.36, W.43 Chain F: Y.23, G.26, M.27, F.30 Chain V: F.4, I.7 Ligands: BCL.1, BCL.8, BCL.11 14 PLIP interactions: 5 interactions with chain A, 3 interactions with chain V, 3 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: A:F.23, A:F.23, A:L.24, A:L.24, A:L.27, V:F.4, V:I.7, V:I.7, E:F.25, E:L.36, E:W.43, F:M.27, F:F.30, F:F.30 SPO.10: 17 residues within 4Å: Chain A: F.4, I.7 Chain E: F.17, Q.20, L.24, L.27, M.34 Chain T: F.25, A.28, H.32, L.36 Chain U: Y.23, G.26, M.27 Ligands: BCL.8, BCL.28, BCL.29 12 PLIP interactions: 6 interactions with chain E, 1 interactions with chain U, 2 interactions with chain A, 3 interactions with chain T Hydrophobic interactions: E:F.17, E:F.17, E:Q.20, E:L.24, E:L.27, E:L.27, U:Y.23, A:F.4, A:I.7, T:F.25, T:A.28, T:H.32 SPO.15: 24 residues within 4Å: Chain 6: Q.20, F.23, L.24, L.27, I.31, M.34 Chain 7: L.6 Chain I: F.25, A.28, H.32, W.43 Chain J: E.18, L.19, V.22, Y.23, G.26, M.27, F.30 Chain K: F.4, K.6, I.7, I.10 Ligands: BCL.14, BCL.16 20 PLIP interactions: 4 interactions with chain K, 7 interactions with chain J, 6 interactions with chain 6, 3 interactions with chain I Hydrophobic interactions: K:F.4, K:K.6, K:I.7, K:I.10, J:E.18, J:L.19, J:V.22, J:Y.23, J:Y.23, J:M.27, J:F.30, 6:F.23, 6:F.23, 6:L.24, 6:L.27, 6:L.27, 6:I.31, I:F.25, I:A.28, I:H.32 SPO.21: 22 residues within 4Å: Chain M: F.17, Q.20, L.24, L.27, M.30, I.31, M.34 Chain V: F.25, A.28, H.32, W.43 Chain W: V.22, Y.23, G.26, M.27 Chain Z: F.4, K.6, I.7, I.10 Ligands: BCL.20, BCL.30, BCL.31 12 PLIP interactions: 4 interactions with chain M, 3 interactions with chain V, 3 interactions with chain W, 2 interactions with chain Z Hydrophobic interactions: M:F.17, M:L.24, M:L.27, M:I.31, V:F.25, V:A.28, V:H.32, W:V.22, W:Y.23, W:M.27, Z:F.4, Z:I.10 SPO.22: 21 residues within 4Å: Chain 6: K.6, I.7, I.10 Chain I: F.17, F.23, L.24, L.27, I.31 Chain O: A.28, H.32, L.36, W.43 Chain P: L.19, V.22, Y.23, G.26, M.27, F.30, I.31 Ligands: BCL.23, BCL.57 18 PLIP interactions: 7 interactions with chain P, 6 interactions with chain I, 3 interactions with chain 6, 2 interactions with chain O Hydrophobic interactions: P:L.19, P:L.19, P:V.22, P:Y.23, P:M.27, P:F.30, P:I.31, I:F.23, I:L.24, I:L.24, I:L.27, I:L.27, I:I.31, 6:K.6, 6:I.7, 6:I.10, O:A.28, O:H.32 SPO.26: 25 residues within 4Å: Chain G: F.17, Q.20, F.23, L.27, M.34 Chain K: F.25, A.28, V.29, H.32, L.33, L.36 Chain L: V.22, Y.23, Q.25, G.26, M.27, F.30 Chain S: K.12, A.16, A.20, M.23 Ligands: BCL.12, U10.13, BCL.17, BCL.19 14 PLIP interactions: 4 interactions with chain G, 4 interactions with chain L, 2 interactions with chain S, 4 interactions with chain K Hydrophobic interactions: G:F.17, G:F.17, G:F.23, G:L.27, L:Y.23, L:Q.25, L:M.27, L:F.30, S:A.16, S:A.20, K:A.28, K:V.29, K:H.32, K:L.36 SPO.27: 18 residues within 4Å: Chain C: F.25, H.32 Chain D: Y.23, G.26, M.27, F.30 Chain E: I.7 Chain T: F.17, Q.20, F.23, L.24, L.27, M.30, I.31, M.34 Ligands: BCL.4, BCL.7, BCL.28 12 PLIP interactions: 7 interactions with chain T, 1 interactions with chain C, 3 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: T:Q.20, T:F.23, T:F.23, T:L.24, T:L.27, T:L.27, T:I.31, C:F.25, D:Y.23, D:F.30, D:F.30, E:I.7 SPO.34: 20 residues within 4Å: Chain 2: L.106 Chain M: F.25, H.32, L.33 Chain N: Y.23, G.26, M.27, F.30 Chain X: F.4, I.7 Chain Z: F.17, Q.20, F.23, L.24, L.27, M.30, M.34 Ligands: BCL.20, BCL.36, SPO.50 16 PLIP interactions: 5 interactions with chain M, 5 interactions with chain Z, 3 interactions with chain N, 2 interactions with chain X, 1 interactions with chain 2 Hydrophobic interactions: M:F.25, M:H.32, M:L.33, M:L.33, M:L.33, Z:F.17, Z:F.17, Z:F.23, Z:L.24, Z:L.27, N:Y.23, N:M.27, N:F.30, X:F.4, X:I.7, 2:L.106 SPO.38: 15 residues within 4Å: Chain 0: Y.23, G.26, M.27, L.29, F.30 Chain X: Q.20, L.24, L.27, M.34 Chain Z: A.28, V.29, H.32 Ligands: BCL.32, BCL.35, BCL.37 8 PLIP interactions: 4 interactions with chain 0, 2 interactions with chain X, 2 interactions with chain Z Hydrophobic interactions: 0:Y.23, 0:M.27, 0:L.29, 0:F.30, X:L.24, X:L.27, Z:A.28, Z:V.29 SPO.50: 26 residues within 4Å: Chain 2: F.68, V.71, G.72, F.75, I.76, F.86, W.116, L.117, S.120, F.121, L.123, M.124, M.158, F.159, L.161, S.162, F.163, W.172, V.176, Y.178, G.179, I.180, H.183 Ligands: SPO.34, BPH.47, BCL.51 16 PLIP interactions: 16 interactions with chain 2 Hydrophobic interactions: 2:F.68, 2:V.71, 2:I.76, 2:W.116, 2:L.117, 2:F.121, 2:F.121, 2:L.123, 2:M.124, 2:F.159, 2:L.161, 2:W.172, 2:V.176, 2:Y.178, 2:Y.178, 2:I.180 SPO.56: 21 residues within 4Å: Chain 4: F.17, Q.20, G.21, L.24, L.27, M.34 Chain O: F.4, I.7 Chain X: F.25, A.28, V.29, H.32, L.36, W.43 Chain Y: Y.23, G.26, M.27, F.30 Ligands: BCL.32, BCL.33, BCL.55 16 PLIP interactions: 4 interactions with chain Y, 4 interactions with chain 4, 3 interactions with chain O, 5 interactions with chain X Hydrophobic interactions: Y:M.27, Y:F.30, Y:F.30, Y:F.30, 4:F.17, 4:Q.20, 4:L.24, 4:L.27, O:F.4, O:I.7, O:I.7, X:F.25, X:A.28, X:V.29, X:H.32, X:W.43 SPO.58: 20 residues within 4Å: Chain 4: A.28, H.32, L.36 Chain 5: V.22, Y.23, G.26, M.27, F.30 Chain I: F.4, I.7 Chain O: F.17, Q.20, F.23, L.24, L.27, I.31, M.34 Ligands: BCL.55, BCL.57, BCL.59 15 PLIP interactions: 7 interactions with chain O, 2 interactions with chain I, 2 interactions with chain 4, 4 interactions with chain 5 Hydrophobic interactions: O:F.17, O:F.17, O:F.17, O:F.23, O:L.24, O:L.24, O:L.27, I:F.4, I:I.7, 4:A.28, 4:L.36, 5:Y.23, 5:Y.23, 5:M.27, 5:F.30 SPO.62: 21 residues within 4Å: Chain 6: H.32, L.36, W.43 Chain 7: L.19, V.22, Y.23, G.26, M.27, F.30 Chain G: F.4, K.6, I.10 Chain K: F.17, Q.20, F.23, L.24, L.27, M.34 Chain L: L.6 Ligands: BCL.18, BCL.60 15 PLIP interactions: 4 interactions with chain G, 4 interactions with chain 7, 5 interactions with chain K, 1 interactions with chain 6, 1 interactions with chain L Hydrophobic interactions: G:F.4, G:K.6, G:K.6, G:I.10, 7:L.19, 7:V.22, 7:Y.23, 7:F.30, K:F.17, K:F.23, K:L.24, K:L.24, K:L.27, 6:H.32, L:L.6

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

U10.13: 27 residues within 4Å: Chain 1: F.23, V.37, F.41, F.42, A.78, L.81, V.89, L.92, C.93 Chain G: I.7, W.8, F.11, Q.20, L.26, M.30, L.33, M.34, S.37 Chain K: F.17, V.18, G.21, V.22, F.25, L.33 Chain L: Y.23 Ligands: BCL.17, SPO.26 19 PLIP interactions: 9 interactions with chain G, 4 interactions with chain K, 6 interactions with chain 1 Hydrophobic interactions: G:I.7, G:W.8, G:F.11, G:F.11, G:L.26, G:L.26, G:L.33, G:M.34, K:V.18, K:V.22, K:F.25, K:L.33, 1:F.23, 1:V.37, 1:F.41, 1:F.41, 1:F.41, 1:F.41 Hydrogen bonds: G:S.37 U10.41: 17 residues within 4Å: Chain 1: S.179, L.180, T.183, L.186, A.187, L.190, H.191, L.194, F.217, S.224, V.225, G.226, I.230, L.233 Ligands: U10.42, BPH.44, BCL.51 8 PLIP interactions: 8 interactions with chain 1 Hydrophobic interactions: 1:L.180, 1:T.183, 1:L.186, 1:A.187, 1:L.190, 1:I.230 Hydrogen bonds: 1:V.225 pi-Stacking: 1:F.217 U10.42: 12 residues within 4Å: Chain 1: P.172, L.173, M.175, L.176, S.179, V.255, W.263, W.264 Chain 2: F.91, I.180 Ligands: U10.41, BCL.51 7 PLIP interactions: 7 interactions with chain 1 Hydrophobic interactions: 1:P.172, 1:P.172, 1:M.175, 1:L.176, 1:W.263, 1:W.264 Hydrogen bonds: 1:S.179 U10.43: 7 residues within 4Å: Chain 1: D.265, W.266, N.269, L.270, P.271 Chain E: M.30 Chain T: S.37 No protein-ligand interaction detected (PLIP) U10.49: 25 residues within 4Å: Chain 1: V.27, F.30, Y.31, V.32, V.40, W.101, R.104 Chain 2: M.215, M.219, H.220, T.223, A.249, A.250, W.253, M.257, F.259, N.260, A.261, T.262, I.266, W.269 Ligands: BCL.39, BPH.40, BCL.45, 3PE.54 19 PLIP interactions: 9 interactions with chain 1, 10 interactions with chain 2 Hydrophobic interactions: 1:V.27, 1:F.30, 1:F.30, 1:F.30, 1:F.30, 1:V.32, 1:V.32, 1:V.40, 1:W.101, 2:M.219, 2:W.253, 2:M.257, 2:F.259, 2:A.261, 2:I.266, 2:I.266, 2:W.269, 2:W.269 Hydrogen bonds: 2:A.261 U10.52: 9 residues within 4Å: Chain 1: W.264, W.267, Y.268 Chain 2: L.87, R.88, E.89, L.90, F.91, F.181 6 PLIP interactions: 4 interactions with chain 2, 2 interactions with chain 1 Hydrophobic interactions: 2:F.91, 1:W.267 Hydrogen bonds: 2:L.90, 2:F.91 pi-Stacking: 2:F.91, 1:W.267

3 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.40: 29 residues within 4Å: Chain 1: A.43, T.47, I.50, V.90, A.97, F.98, W.101, E.105, I.118, A.121, F.122, A.125, Y.129, Y.149, G.150, V.151, H.154, L.239, A.242 Chain 2: Y.211, T.214, M.215, A.218, M.219, W.253, M.257 Ligands: BCL.39, BCL.45, U10.49 15 PLIP interactions: 12 interactions with chain 1, 3 interactions with chain 2 Hydrophobic interactions: 1:A.43, 1:I.50, 1:V.90, 1:A.97, 1:A.121, 1:F.122, 1:F.122, 1:F.122, 1:A.125, 1:Y.149, 1:L.239, 1:A.242, 2:Y.211, 2:T.214, 2:A.218 BPH.44: 11 residues within 4Å: Chain 1: V.221, G.222, Y.223 Chain 2: T.31, L.48, G.49, I.51, L.61, W.130 Ligands: U10.41, BPH.47 9 PLIP interactions: 5 interactions with chain 2, 4 interactions with chain 1 Hydrophobic interactions: 2:L.48, 2:I.51, 2:L.61, 2:W.130, 2:W.130, 1:V.221, 1:Y.223 Hydrogen bonds: 1:V.221, 1:V.221 BPH.47: 24 residues within 4Å: Chain 1: F.182, T.185, L.186, L.190, L.220, V.221 Chain 2: G.64, A.65, F.68, F.69, S.126, W.130, T.134, T.147, A.150, F.151, A.154, A.274, V.275, P.278 Ligands: BPH.44, BCL.46, SPO.50, BCL.51 15 PLIP interactions: 3 interactions with chain 1, 12 interactions with chain 2 Hydrophobic interactions: 1:F.182, 1:T.185, 1:L.186, 2:A.65, 2:F.68, 2:F.68, 2:F.69, 2:F.69, 2:W.130, 2:A.150, 2:F.151, 2:F.151, 2:F.151, 2:F.151, 2:P.278

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

FE.48: 5 residues within 4Å: Chain 1: H.191, H.231 Chain 2: H.220, E.235, H.267 5 PLIP interactions: 2 interactions with chain 1, 3 interactions with chain 2 Metal complexes: 1:H.191, 1:H.231, 2:H.220, 2:E.235, 2:H.267

3 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.53: 20 residues within 4Å: Chain 1: N.200, P.201 Chain 2: G.144, K.145, H.146, W.149, A.152, G.153, W.156, R.268, W.271, W.272, V.279, I.283 Chain 3: S.19, F.23, L.26, L.27, Y.30 Chain 4: L.26 22 PLIP interactions: 12 interactions with chain 2, 9 interactions with chain 3, 1 interactions with chain 4 Hydrophobic interactions: 2:W.149, 2:A.152, 2:W.156, 2:W.156, 2:W.156, 2:W.271, 2:W.272, 2:W.272, 2:V.279, 3:F.23, 3:F.23, 3:L.26, 3:L.26, 3:L.27, 3:L.27, 3:Y.30, 3:Y.30, 3:Y.30, 4:L.26 Hydrogen bonds: 2:K.145 Salt bridges: 2:H.146, 2:R.268 3PE.54: 18 residues within 4Å: Chain 2: A.208, R.254, G.258, F.259, W.269, F.273 Chain 3: F.24, V.28, Q.32, M.36, Y.40, Q.53, G.54, P.55, F.56 Ligands: BCL.45, U10.49, 3PE.61 11 PLIP interactions: 5 interactions with chain 3, 6 interactions with chain 2 Hydrophobic interactions: 3:F.24, 3:V.28, 3:Q.32, 2:A.208, 2:F.259, 2:F.259, 2:W.269, 2:F.273 Hydrogen bonds: 3:Q.53, 3:F.56 Salt bridges: 2:R.254 3PE.61: 15 residues within 4Å: Chain 1: V.27, G.28 Chain 3: N.52, D.94 Chain 6: D.12, R.14, R.15, V.18, A.19, G.21, V.22, L.26 Chain K: R.15 Ligands: 3PE.54, BCL.60 9 PLIP interactions: 6 interactions with chain 6, 1 interactions with chain 3, 2 interactions with chain K Hydrophobic interactions: 6:A.19, 6:V.22, 6:V.22, 6:L.26 Salt bridges: 6:R.14, 6:R.15, K:R.15, K:R.15 Hydrogen bonds: 3:N.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bracun, L. et al., Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-angstrom resolution. Sci Adv (2021)

Release Date

2021-06-30

Peptides

Antenna pigment protein alpha chain: ACEGIKMOQTVXZ46
Antenna pigment protein beta chain: BDFHJLNPRUWY057
PufX: S
Photosynthetic reaction center L subunit: 1
Reaction center protein M chain: 2
Photosynthetic reaction center subunit H: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
o

C
t

E
r

G
a

I
e

K
b

M
k

O
f

Q
u

T
s

V
n

X
i

Z
j

4
g

6
d

B
N

D
S

F
O

H
U

J
D

L
A

N
J

P
E

R
T

U
R

W
K

Y
G

0
I

5
F

7
B

S
X

1
L

2
M

3
H

Membrane

We predict this structure to be a membrane protein.
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Antenna pigment protein alpha chain

Antenna pigment protein beta chain

PufX

Photosynthetic reaction center L subunit

Reaction center protein M chain

Photosynthetic reaction center subunit H