SMTL ID : 8b64.1

Cryo-EM structure of RC-LH1-PufX photosynthetic core complex from Rba. capsulatus

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: 14 residues within 4Å: Chain A: L.24, A.28, H.32, L.35, W.43 Chain E: F.31, V.34, A.35, A.38, H.39, V.42 Chain G: M.26 Ligands: SPO.9, BCL.10 8 PLIP interactions: 2 interactions with chain E, 5 interactions with chain A, 1 interactions with chain G, Hydrophobic interactions: E:A.38, E:V.42, A:L.24, A:L.35, A:W.43, A:W.43, G:M.26 Metal complexes: A:H.32 BCL.2: 27 residues within 4Å: Chain B: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain C: H.21, Y.24, F.49 Chain F: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain K: I.7, V.16, Q.20, F.23, I.31 Ligands: BCL.3, BCL.4, SPO.12, SPO.32, 3PE.34 15 PLIP interactions: 5 interactions with chain K, 1 interactions with chain C, 2 interactions with chain F, 7 interactions with chain B, Hydrophobic interactions: K:I.7, K:V.16, K:F.23, K:F.23, K:I.31, C:F.49, F:A.38, F:W.45, B:L.24, B:F.25, B:L.35, B:W.43, B:W.43, B:W.43, B:W.43 BCL.3: 21 residues within 4Å: Chain 7: W.43 Chain B: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain F: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Ligands: BCL.2, SPO.11, SPO.13, BCL.74 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain F, Hydrophobic interactions: B:I.31, B:I.31, B:F.41, F:F.31, F:I.32, F:A.35, F:V.36, F:V.42, F:W.48, F:W.48, F:W.48, F:W.48, F:F.49, F:F.49 Metal complexes: F:H.39 BCL.4: 20 residues within 4Å: Chain C: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Chain K: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.2, SPO.12, BCL.31, SPO.32 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain K, Hydrophobic interactions: C:F.31, C:I.32, C:A.35, C:V.36, C:V.42, C:W.48, C:W.48, C:W.48, C:F.49, C:F.49, K:I.31, K:F.41 Metal complexes: C:H.39 BCL.6: 25 residues within 4Å: Chain A: I.7, W.8, V.16, Q.20, F.23, I.31 Chain D: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain E: Y.24, F.49 Chain L: F.31, V.34, A.35, A.38, H.39, V.42 Ligands: BCL.7, SPO.9, BCL.10, SPO.35 18 PLIP interactions: 7 interactions with chain A, 2 interactions with chain L, 2 interactions with chain E, 7 interactions with chain D, Hydrophobic interactions: A:I.7, A:W.8, A:V.16, A:F.23, A:F.23, A:I.31, A:I.31, L:A.38, L:V.42, E:Y.24, E:F.49, D:L.24, D:F.25, D:L.35, D:W.43, D:W.43, D:W.43, D:W.43 BCL.7: 20 residues within 4Å: Chain D: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain L: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Ligands: SPO.5, BCL.6, SPO.8, BCL.31 13 PLIP interactions: 10 interactions with chain L, 3 interactions with chain D, Hydrophobic interactions: L:F.31, L:I.32, L:A.35, L:V.36, L:V.42, L:W.48, L:W.48, L:W.48, L:F.49, D:I.31, D:I.31, D:F.41 Metal complexes: L:H.39 BCL.10: 21 residues within 4Å: Chain A: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain D: W.43, L.44 Chain E: F.31, I.32, A.35, V.36, H.39, V.42, W.48, F.49 Ligands: BCL.1, BCL.6, SPO.9, SPO.35 16 PLIP interactions: 4 interactions with chain A, 11 interactions with chain E, 1 interactions with chain D, Hydrophobic interactions: A:I.31, A:I.31, A:L.35, A:F.41, E:F.31, E:A.35, E:V.36, E:V.42, E:W.48, E:W.48, E:W.48, E:W.48, E:F.49, E:F.49, D:L.44 Metal complexes: E:H.39 BCL.14: 28 residues within 4Å: Chain H: F.98, A.125, I.126, A.128, L.132, V.158, T.161, G.162, Y.163, N.167, F.168, H.169, H.174, I.178, F.181, F.182, S.245, A.246, C.248, M.249 Chain I: F.196, Y.209 Ligands: BPH.15, 3PE.19, BCL.20, U10.22, BCL.24, BCL.26 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain I, Hydrophobic interactions: H:F.98, H:F.98, H:A.125, H:T.161, H:Y.163, H:F.168, H:I.178, H:F.181, H:F.182, I:F.196, I:Y.209 Hydrogen bonds: H:S.245 BCL.20: 21 residues within 4Å: Chain H: F.47, I.50, Y.129, L.132, F.147, I.151, W.152, H.154, L.155 Chain I: F.196, G.202, I.205, A.206, Y.209, G.210, L.213 Ligands: BCL.14, BPH.15, BCL.26, 3PE.29, 3PE.30 13 PLIP interactions: 6 interactions with chain I, 7 interactions with chain H, Hydrophobic interactions: I:F.196, I:I.205, I:I.205, I:A.206, I:L.213, H:F.47, H:I.50, H:Y.129, H:L.132, H:F.147, H:L.155 pi-Stacking: I:Y.209 Metal complexes: H:H.154 BCL.24: 19 residues within 4Å: Chain H: H.169, M.175, I.178, S.179, F.182, T.183 Chain I: M.121, W.156, L.159, I.178, H.181, L.182, T.185 Ligands: BCL.14, U10.16, U10.17, SPO.23, BCL.26, BPH.27 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain H, Hydrophobic interactions: I:L.159, I:I.178, I:L.182, H:I.178, H:I.178, H:T.183 BCL.26: 28 residues within 4Å: Chain H: V.158, Y.163, H.169, F.182 Chain I: M.121, F.149, A.152, L.155, W.156, L.159, T.185, N.186, F.188, S.189, L.195, F.196, H.201, S.204, I.205, L.208, Y.209, V.275, G.279, I.283 Ligands: BCL.14, BCL.20, BCL.24, BPH.27 14 PLIP interactions: 11 interactions with chain I, 3 interactions with chain H, Hydrophobic interactions: I:F.149, I:A.152, I:L.155, I:W.156, I:T.185, I:F.188, I:L.195, I:F.196, I:I.205, I:L.208, I:Y.209, H:V.158, H:F.182 pi-Cation interactions: H:H.169 BCL.31: 24 residues within 4Å: Chain C: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain D: Q.20, F.23, I.31 Chain K: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain L: Y.24, F.49 Ligands: BCL.4, SPO.5, BCL.7, SPO.8, 3PE.33 14 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D, 6 interactions with chain K, 2 interactions with chain L, Hydrophobic interactions: C:A.38, C:W.45, D:F.23, D:F.23, D:F.23, D:I.31, K:L.24, K:F.25, K:L.35, K:W.43, K:W.43, K:W.43, L:Y.24, L:F.49 BCL.36: 14 residues within 4Å: Chain M: A.28, H.32, W.43 Chain N: F.49 Chain O: F.31, V.34, A.35, A.38, H.39, V.42 Chain P: I.31 Ligands: SPO.38, BCL.40, BCL.41 6 PLIP interactions: 4 interactions with chain M, 1 interactions with chain P, 1 interactions with chain N, Hydrophobic interactions: M:W.43, M:W.43, M:W.43, M:W.43, P:I.31, N:F.49 BCL.40: 15 residues within 4Å: Chain M: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain O: F.31, A.35, H.39, W.48, F.49 Ligands: BCL.36, SPO.37, BCL.44 8 PLIP interactions: 3 interactions with chain M, 5 interactions with chain O, Hydrophobic interactions: M:I.31, M:I.31, M:F.41, O:F.31, O:A.35, O:W.48 pi-Cation interactions: O:H.39 Metal complexes: O:H.39 BCL.41: 17 residues within 4Å: Chain N: F.31, I.32, A.35, H.39, V.42, W.48, F.49 Chain P: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.36, SPO.38, BCL.42 10 PLIP interactions: 3 interactions with chain P, 7 interactions with chain N, Hydrophobic interactions: P:I.31, P:I.31, P:F.41, N:F.31, N:A.35, N:V.42, N:W.48, N:W.48 pi-Cation interactions: N:H.39 Metal complexes: N:H.39 BCL.42: 16 residues within 4Å: Chain N: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain P: A.28, H.32, W.43 Chain S: I.31 Chain U: F.49 Ligands: SPO.39, BCL.41, SPO.46, BCL.47 9 PLIP interactions: 5 interactions with chain P, 1 interactions with chain S, 1 interactions with chain U, 2 interactions with chain N, Hydrophobic interactions: P:W.43, P:W.43, P:W.43, P:W.43, S:I.31, U:F.49, N:A.38, N:W.45 Metal complexes: P:H.32 BCL.43: 10 residues within 4Å: Chain Q: F.31, A.35, H.39, V.42 Chain R: L.27, I.31, H.32, L.35, F.41 Ligands: BCL.44 4 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain R, Hydrophobic interactions: Q:V.42, R:I.31, R:F.41 Metal complexes: Q:H.39 BCL.44: 15 residues within 4Å: Chain O: F.49 Chain Q: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain R: L.24, A.28, H.32, W.43 Ligands: SPO.37, BCL.40, BCL.43 9 PLIP interactions: 3 interactions with chain Q, 5 interactions with chain R, 1 interactions with chain O, Hydrophobic interactions: Q:A.38, Q:W.45, R:A.28, R:W.43, R:W.43, R:W.43, O:F.49 Hydrogen bonds: Q:H.39 pi-Stacking: R:H.32 BCL.45: 20 residues within 4Å: Chain S: L.24, F.25, A.28, H.32, L.35, W.43 Chain T: F.49 Chain U: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain V: F.23, I.31 Ligands: BCL.47, BCL.48, SPO.50, SPO.52 12 PLIP interactions: 3 interactions with chain V, 6 interactions with chain S, 2 interactions with chain U, 1 interactions with chain T, Hydrophobic interactions: V:F.23, V:I.31, V:I.31, S:L.24, S:F.25, S:L.35, S:W.43, S:W.43, S:W.43, U:A.38, U:W.45, T:F.49 BCL.47: 17 residues within 4Å: Chain S: L.24, L.27, A.28, I.31, H.32, L.35 Chain U: F.31, I.32, A.35, H.39, V.42, W.48, F.49 Ligands: SPO.39, BCL.42, BCL.45, SPO.46 11 PLIP interactions: 9 interactions with chain U, 2 interactions with chain S, Hydrophobic interactions: U:F.31, U:A.35, U:V.42, U:W.48, U:W.48, U:W.48, U:W.48, S:I.31, S:I.31 pi-Cation interactions: U:H.39 Metal complexes: U:H.39 BCL.48: 20 residues within 4Å: Chain S: W.43 Chain T: F.31, I.32, A.35, V.36, H.39, V.42, W.48, F.49 Chain V: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.45, SPO.50, BCL.51, SPO.52 15 PLIP interactions: 4 interactions with chain V, 11 interactions with chain T, Hydrophobic interactions: V:I.31, V:I.31, V:L.35, V:F.41, T:F.31, T:I.32, T:A.35, T:V.36, T:V.42, T:W.48, T:W.48, T:W.48, T:F.49 pi-Cation interactions: T:H.39 Metal complexes: T:H.39 BCL.51: 25 residues within 4Å: Chain T: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain V: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain W: Q.20, F.23, I.31 Chain Y: H.21, Y.24, L.28, F.49 Ligands: BCL.48, SPO.49, BCL.54, SPO.58 16 PLIP interactions: 3 interactions with chain Y, 8 interactions with chain V, 2 interactions with chain T, 3 interactions with chain W, Hydrophobic interactions: Y:Y.24, Y:L.28, Y:F.49, V:L.24, V:L.24, V:F.25, V:L.35, V:W.43, V:W.43, V:W.43, V:W.43, T:A.38, T:W.45, W:F.23, W:F.23, W:I.31 BCL.53: 25 residues within 4Å: Chain W: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain X: H.21, Y.24, F.49 Chain Y: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain Z: I.7, Q.20, F.23, I.31 Ligands: BCL.54, SPO.55, BCL.56, SPO.60 13 PLIP interactions: 4 interactions with chain Z, 2 interactions with chain Y, 1 interactions with chain X, 6 interactions with chain W, Hydrophobic interactions: Z:I.7, Z:F.23, Z:F.23, Z:I.31, Y:A.38, Y:W.45, X:F.49, W:L.24, W:L.35, W:W.43, W:W.43, W:W.43, W:W.43 BCL.54: 20 residues within 4Å: Chain W: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain Y: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Ligands: SPO.49, BCL.51, BCL.53, SPO.58 13 PLIP interactions: 9 interactions with chain Y, 4 interactions with chain W, Hydrophobic interactions: Y:F.31, Y:I.32, Y:A.35, Y:V.36, Y:V.42, Y:W.48, Y:W.48, Y:W.48, W:I.31, W:I.31, W:L.35, W:F.41 Metal complexes: Y:H.39 BCL.56: 19 residues within 4Å: Chain X: F.31, I.32, A.35, V.36, H.39, V.42, W.48, F.49 Chain Z: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.53, SPO.55, BCL.59, SPO.60 14 PLIP interactions: 10 interactions with chain X, 4 interactions with chain Z, Hydrophobic interactions: X:F.31, X:A.35, X:V.36, X:V.42, X:W.48, X:W.48, X:W.48, X:F.49, X:F.49, Z:I.31, Z:I.31, Z:L.35, Z:F.41 Metal complexes: X:H.39 BCL.59: 25 residues within 4Å: Chain 0: F.4, V.16, Q.20, F.23, I.31 Chain 2: Y.24, L.28, F.49 Chain X: F.31, V.34, A.35, A.38, H.39, V.42 Chain Z: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Ligands: BCL.56, SPO.57, SPO.62, BCL.66 17 PLIP interactions: 3 interactions with chain 2, 7 interactions with chain Z, 1 interactions with chain X, 6 interactions with chain 0, Hydrophobic interactions: 2:Y.24, 2:L.28, 2:F.49, Z:L.24, Z:F.25, Z:L.35, Z:W.43, Z:W.43, Z:W.43, Z:W.43, X:A.38, 0:F.4, 0:V.16, 0:F.23, 0:F.23, 0:I.31, 0:I.31 BCL.61: 24 residues within 4Å: Chain 0: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain 1: H.21, Y.24, F.49 Chain 2: F.31, V.34, A.35, A.38, H.39, V.42 Chain 3: I.7, Q.20, F.23, I.31 Ligands: BCL.63, SPO.65, BCL.66, SPO.68 10 PLIP interactions: 2 interactions with chain 3, 5 interactions with chain 0, 1 interactions with chain 2, 2 interactions with chain 1, Hydrophobic interactions: 3:F.23, 3:I.31, 0:F.25, 0:L.35, 0:W.43, 0:W.43, 0:W.43, 2:A.38, 1:Y.24, 1:F.49 BCL.63: 19 residues within 4Å: Chain 0: W.43 Chain 1: F.31, I.32, A.35, V.36, H.39, W.48, F.49 Chain 3: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.61, SPO.65, BCL.67, SPO.68 13 PLIP interactions: 2 interactions with chain 3, 11 interactions with chain 1, Hydrophobic interactions: 3:I.31, 3:F.41, 1:F.31, 1:I.32, 1:I.32, 1:A.35, 1:V.36, 1:W.48, 1:W.48, 1:W.48, 1:F.49, 1:F.49 Metal complexes: 1:H.39 BCL.66: 21 residues within 4Å: Chain 0: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain 2: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Chain Z: W.43 Ligands: SPO.57, BCL.59, BCL.61, SPO.62 15 PLIP interactions: 4 interactions with chain 0, 11 interactions with chain 2, Hydrophobic interactions: 0:L.27, 0:I.31, 0:I.31, 0:F.41, 2:F.31, 2:I.32, 2:A.35, 2:V.36, 2:V.42, 2:W.48, 2:W.48, 2:W.48, 2:W.48, 2:F.49 Metal complexes: 2:H.39 BCL.67: 24 residues within 4Å: Chain 1: F.31, V.34, A.35, A.38, H.39, V.42 Chain 3: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain 4: F.4, V.16, Q.20, F.23, I.31 Chain 6: Y.24, F.49 Ligands: BCL.63, SPO.64, BCL.70, SPO.73 15 PLIP interactions: 8 interactions with chain 3, 2 interactions with chain 6, 4 interactions with chain 4, 1 interactions with chain 1, Hydrophobic interactions: 3:L.24, 3:F.25, 3:L.35, 3:W.43, 3:W.43, 3:W.43, 3:W.43, 6:Y.24, 6:F.49, 4:F.4, 4:V.16, 4:F.23, 4:I.31, 1:A.38 Metal complexes: 3:H.32 BCL.69: 25 residues within 4Å: Chain 4: G.21, L.24, F.25, A.28, H.32, L.35, W.43 Chain 5: H.21, Y.24, F.49 Chain 6: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Chain 7: I.7, Q.20, F.23, I.31 Ligands: BCL.70, SPO.71, BCL.72, SPO.75 15 PLIP interactions: 4 interactions with chain 7, 2 interactions with chain 6, 7 interactions with chain 4, 2 interactions with chain 5, Hydrophobic interactions: 7:I.7, 7:F.23, 7:F.23, 7:I.31, 6:A.38, 6:W.45, 4:L.24, 4:L.35, 4:W.43, 4:W.43, 4:W.43, 4:W.43, 5:Y.24, 5:F.49 Metal complexes: 4:H.32 BCL.70: 21 residues within 4Å: Chain 3: W.43 Chain 4: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Chain 6: F.31, I.32, A.35, V.36, H.39, V.42, M.43, W.48, F.49 Ligands: SPO.64, BCL.67, BCL.69, SPO.73 13 PLIP interactions: 10 interactions with chain 6, 3 interactions with chain 4, Hydrophobic interactions: 6:F.31, 6:I.32, 6:A.35, 6:V.36, 6:V.42, 6:W.48, 6:W.48, 6:W.48, 6:F.49, 4:I.31, 4:I.31, 4:F.41 Metal complexes: 6:H.39 BCL.72: 19 residues within 4Å: Chain 5: F.31, I.32, A.35, V.36, H.39, V.42, W.48, F.49 Chain 7: L.24, L.27, A.28, I.31, H.32, L.35, F.41 Ligands: BCL.69, SPO.71, BCL.74, SPO.75 14 PLIP interactions: 10 interactions with chain 5, 4 interactions with chain 7, Hydrophobic interactions: 5:F.31, 5:I.32, 5:A.35, 5:V.36, 5:V.42, 5:W.48, 5:W.48, 5:W.48, 5:F.49, 7:I.31, 7:I.31, 7:L.35, 7:F.41 Metal complexes: 5:H.39 BCL.74: 24 residues within 4Å: Chain 5: F.31, V.34, A.35, A.38, H.39, V.42 Chain 7: G.21, F.25, A.28, H.32, L.35, W.43 Chain B: V.16, Q.20, F.23, I.31 Chain F: H.21, Y.24, M.25, F.49 Ligands: BCL.3, SPO.11, SPO.13, BCL.72 14 PLIP interactions: 5 interactions with chain B, 6 interactions with chain 7, 1 interactions with chain 5, 2 interactions with chain F, Hydrophobic interactions: B:V.16, B:F.23, B:F.23, B:F.23, B:I.31, 7:F.25, 7:L.35, 7:W.43, 7:W.43, 7:W.43, 5:A.38, F:Y.24, F:F.49 Metal complexes: 7:H.32

27 x SPO: SPHEROIDENE(Non-covalent)

SPO.5: 12 residues within 4Å: Chain C: F.31, V.34, A.38, A.41, V.42, W.45 Chain K: F.17, Q.20 Chain L: F.49 Ligands: BCL.7, SPO.8, BCL.31 7 PLIP interactions: 5 interactions with chain C, 1 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: C:F.31, C:V.34, C:A.41, C:V.42, C:W.45, L:F.49, K:F.17 SPO.8: 20 residues within 4Å: Chain A: K.6, I.7, V.10 Chain D: Q.20, F.23, L.24, L.27, I.31 Chain K: F.25, H.32 Chain L: L.20, V.23, Y.24, G.27, L.28, F.31 Ligands: SPO.5, BCL.7, BCL.31, SPO.35 19 PLIP interactions: 7 interactions with chain L, 4 interactions with chain A, 6 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: L:L.20, L:V.23, L:V.23, L:Y.24, L:Y.24, L:L.28, L:F.31, A:K.6, A:K.6, A:I.7, A:V.10, D:F.23, D:L.24, D:L.24, D:L.27, D:L.27, D:I.31, K:F.25, K:H.32 SPO.9: 21 residues within 4Å: Chain A: F.23, L.24, L.27, I.34 Chain D: F.25, V.29, H.32 Chain E: V.23, Y.24, S.26, G.27, L.28, A.30, F.31 Chain G: G.19, I.22, M.26 Ligands: BCL.1, BCL.6, BCL.10, SPO.35 9 PLIP interactions: 3 interactions with chain A, 1 interactions with chain G, 3 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: A:F.23, A:L.24, A:L.27, G:I.22, E:A.30, E:F.31, E:F.31, D:F.25, D:H.32 SPO.11: 22 residues within 4Å: Chain 7: F.25, V.29, H.32, L.33 Chain B: F.17, Q.20, L.24, L.27, L.30 Chain F: L.20, V.23, Y.24, G.27, L.28, F.31 Chain K: K.6, I.7, V.10 Ligands: BCL.3, SPO.12, SPO.13, BCL.74 19 PLIP interactions: 6 interactions with chain B, 8 interactions with chain F, 2 interactions with chain 7, 3 interactions with chain K Hydrophobic interactions: B:F.17, B:F.17, B:L.24, B:L.24, B:L.27, B:L.30, F:L.20, F:V.23, F:V.23, F:Y.24, F:Y.24, F:L.28, F:F.31, F:F.31, 7:F.25, 7:H.32, K:K.6, K:I.7, K:V.10 SPO.12: 12 residues within 4Å: Chain B: F.17 Chain C: F.49 Chain F: F.31, V.34, A.38, A.41, V.42, W.45 Ligands: BCL.2, BCL.4, SPO.11, SPO.32 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: F:F.31, F:V.34, F:A.41, F:V.42, F:W.45, C:F.49, C:F.49 SPO.13: 13 residues within 4Å: Chain 5: F.31, V.34, A.38, A.41, V.42, W.45 Chain 7: Q.20, G.21 Chain F: F.49 Ligands: BCL.3, SPO.11, BCL.74, SPO.75 8 PLIP interactions: 5 interactions with chain 5, 3 interactions with chain F Hydrophobic interactions: 5:F.31, 5:V.34, 5:A.38, 5:A.41, 5:V.42, F:F.49, F:F.49, F:F.49 SPO.23: 23 residues within 4Å: Chain I: W.66, F.67, F.68, I.70, G.71, Y.74, W.75, F.85, I.105, Q.115, S.118, L.119, M.121, A.122, W.156, L.159, G.160, W.170, P.174, Y.176, G.177, I.178 Ligands: BCL.24 19 PLIP interactions: 19 interactions with chain I Hydrophobic interactions: I:F.67, I:F.67, I:F.67, I:F.68, I:I.70, I:I.70, I:Y.74, I:Y.74, I:I.105, I:L.119, I:A.122, I:W.156, I:L.159, I:W.170, I:W.170, I:P.174, I:Y.176, I:Y.176, I:I.178 SPO.32: 23 residues within 4Å: Chain B: F.25, H.32, L.33 Chain C: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain D: K.6, I.7, L.9, V.10 Chain K: F.17, Q.20, F.23, L.24, L.27 Chain L: L.7 Ligands: BCL.2, BCL.4, SPO.12 20 PLIP interactions: 5 interactions with chain D, 5 interactions with chain K, 1 interactions with chain B, 8 interactions with chain C, 1 interactions with chain L Hydrophobic interactions: D:K.6, D:K.6, D:I.7, D:L.9, D:V.10, K:F.17, K:F.17, K:F.23, K:L.24, K:L.27, B:F.25, C:E.19, C:L.20, C:V.23, C:V.23, C:Y.24, C:Y.24, C:F.31, C:F.31, L:L.7 SPO.35: 12 residues within 4Å: Chain D: F.17 Chain E: F.49 Chain L: F.31, V.34, A.38, A.41, V.42, W.45 Ligands: BCL.6, SPO.8, SPO.9, BCL.10 8 PLIP interactions: 6 interactions with chain L, 2 interactions with chain E Hydrophobic interactions: L:F.31, L:V.34, L:A.38, L:A.41, L:V.42, L:W.45, E:F.49, E:F.49 SPO.37: 19 residues within 4Å: Chain M: F.17, Q.20, F.23, L.24, L.27, I.34 Chain O: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain R: F.25, H.32, L.36, W.43 Ligands: BCL.40, BCL.44 16 PLIP interactions: 2 interactions with chain R, 8 interactions with chain O, 6 interactions with chain M Hydrophobic interactions: R:F.25, R:W.43, O:E.19, O:L.20, O:V.23, O:V.23, O:Y.24, O:L.28, O:F.31, O:F.31, M:F.17, M:F.17, M:F.23, M:L.24, M:L.24, M:L.27 SPO.38: 16 residues within 4Å: Chain M: F.25, H.32, L.33 Chain N: L.20, V.23, Y.24, G.27, L.28, F.31 Chain P: Q.20, F.23, L.24, L.27 Ligands: BCL.36, SPO.39, BCL.41 19 PLIP interactions: 2 interactions with chain M, 12 interactions with chain N, 5 interactions with chain P Hydrophobic interactions: M:F.25, M:H.32, N:L.20, N:L.20, N:V.23, N:V.23, N:Y.24, N:Y.24, N:Y.24, N:L.28, N:L.28, N:L.28, N:F.31, N:F.31, P:F.23, P:F.23, P:L.24, P:L.27, P:L.27 SPO.39: 13 residues within 4Å: Chain N: F.31, V.34, A.38, A.41, V.42, W.45 Chain P: G.21, L.24 Chain U: F.49 Ligands: SPO.38, BCL.42, SPO.46, BCL.47 10 PLIP interactions: 7 interactions with chain N, 1 interactions with chain P, 2 interactions with chain U Hydrophobic interactions: N:F.31, N:V.34, N:A.38, N:A.41, N:V.42, N:W.45, N:W.45, P:L.24, U:F.49, U:F.49 SPO.46: 20 residues within 4Å: Chain P: F.25, H.32 Chain S: F.17, Q.20, F.23, L.24, L.27 Chain U: L.20, V.23, Y.24, G.27, L.28, F.31 Chain V: K.6, I.7, V.10 Ligands: SPO.39, BCL.42, BCL.47, SPO.50 23 PLIP interactions: 12 interactions with chain U, 2 interactions with chain P, 6 interactions with chain S, 3 interactions with chain V Hydrophobic interactions: U:L.20, U:L.20, U:V.23, U:V.23, U:Y.24, U:Y.24, U:Y.24, U:L.28, U:L.28, U:F.31, U:F.31, U:F.31, P:F.25, P:H.32, S:F.17, S:F.23, S:F.23, S:L.24, S:L.27, S:L.27, V:K.6, V:I.7, V:V.10 SPO.49: 13 residues within 4Å: Chain T: F.31, V.34, A.38, A.41, V.42, W.45 Chain V: F.17, Q.20 Chain Y: F.49 Ligands: BCL.51, SPO.52, BCL.54, SPO.58 8 PLIP interactions: 6 interactions with chain T, 2 interactions with chain Y Hydrophobic interactions: T:F.31, T:V.34, T:A.38, T:A.41, T:V.42, T:W.45, Y:F.49, Y:F.49 SPO.50: 12 residues within 4Å: Chain S: Q.20 Chain T: F.49 Chain U: F.31, V.34, A.38, A.41, V.42, W.45 Ligands: BCL.45, SPO.46, BCL.48, SPO.52 7 PLIP interactions: 2 interactions with chain T, 5 interactions with chain U Hydrophobic interactions: T:F.49, T:F.49, U:F.31, U:V.34, U:A.38, U:A.41, U:V.42 SPO.52: 24 residues within 4Å: Chain S: F.25, H.32, L.33 Chain T: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain V: F.17, Q.20, F.23, L.24, L.27, I.31 Chain W: F.4, K.6, I.7, V.10 Ligands: BCL.45, BCL.48, SPO.49, SPO.50 21 PLIP interactions: 4 interactions with chain W, 9 interactions with chain V, 7 interactions with chain T, 1 interactions with chain S Hydrophobic interactions: W:F.4, W:K.6, W:K.6, W:I.7, V:F.17, V:F.17, V:F.23, V:F.23, V:L.24, V:L.24, V:L.27, V:L.27, V:I.31, T:E.19, T:L.20, T:V.23, T:V.23, T:V.23, T:L.28, T:F.31, S:F.25 SPO.55: 13 residues within 4Å: Chain W: F.17, Q.20 Chain X: F.49 Chain Y: F.31, V.34, A.38, A.41, V.42, W.45 Ligands: BCL.53, BCL.56, SPO.58, SPO.60 8 PLIP interactions: 4 interactions with chain Y, 3 interactions with chain X, 1 interactions with chain W Hydrophobic interactions: Y:F.31, Y:V.34, Y:A.38, Y:V.42, X:F.49, X:F.49, X:F.49, W:F.17 SPO.57: 11 residues within 4Å: Chain 2: F.49 Chain X: F.31, V.34, A.38, A.41, V.42, W.45 Chain Z: Q.20 Ligands: BCL.59, SPO.60, BCL.66 7 PLIP interactions: 5 interactions with chain X, 2 interactions with chain 2 Hydrophobic interactions: X:F.31, X:V.34, X:A.38, X:A.41, X:V.42, 2:F.49, 2:F.49 SPO.58: 23 residues within 4Å: Chain V: F.25, V.29, H.32 Chain W: F.17, Q.20, F.23, L.24, L.27 Chain X: L.7 Chain Y: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain Z: K.6, I.7, V.10 Ligands: SPO.49, BCL.51, BCL.54, SPO.55 21 PLIP interactions: 7 interactions with chain W, 8 interactions with chain Y, 4 interactions with chain Z, 1 interactions with chain X, 1 interactions with chain V Hydrophobic interactions: W:F.17, W:F.17, W:F.23, W:F.23, W:L.24, W:L.27, W:L.27, Y:E.19, Y:L.20, Y:L.20, Y:Y.24, Y:Y.24, Y:Y.24, Y:L.28, Y:F.31, Z:K.6, Z:K.6, Z:I.7, Z:V.10, X:L.7, V:F.25 SPO.60: 22 residues within 4Å: Chain 0: K.6, I.7 Chain 2: L.7 Chain W: F.25, V.29, H.32 Chain X: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain Z: F.17, Q.20, F.23, L.24, L.27 Ligands: BCL.53, SPO.55, BCL.56, SPO.57 24 PLIP interactions: 8 interactions with chain Z, 3 interactions with chain 0, 10 interactions with chain X, 2 interactions with chain W, 1 interactions with chain 2 Hydrophobic interactions: Z:F.17, Z:F.17, Z:F.23, Z:F.23, Z:L.24, Z:L.24, Z:L.27, Z:L.27, 0:K.6, 0:K.6, 0:I.7, X:E.19, X:L.20, X:V.23, X:V.23, X:V.23, X:Y.24, X:Y.24, X:L.28, X:F.31, X:F.31, W:F.25, W:H.32, 2:L.7 SPO.62: 20 residues within 4Å: Chain 0: F.17, Q.20, F.23, L.24, L.27 Chain 2: L.20, V.23, Y.24, G.27, L.28, F.31 Chain 3: K.6, I.7, V.10 Chain Z: F.25, H.32, L.33 Ligands: BCL.59, SPO.65, BCL.66 21 PLIP interactions: 10 interactions with chain 2, 3 interactions with chain 3, 6 interactions with chain 0, 2 interactions with chain Z Hydrophobic interactions: 2:L.20, 2:L.20, 2:V.23, 2:V.23, 2:Y.24, 2:Y.24, 2:Y.24, 2:L.28, 2:F.31, 2:F.31, 3:K.6, 3:I.7, 3:V.10, 0:F.17, 0:F.17, 0:F.23, 0:L.24, 0:L.27, 0:L.27, Z:F.25, Z:H.32 SPO.64: 13 residues within 4Å: Chain 1: F.31, V.34, A.38, A.41, V.42, W.45 Chain 3: Q.20, G.21 Chain 6: F.49 Ligands: BCL.67, SPO.68, BCL.70, SPO.73 8 PLIP interactions: 6 interactions with chain 1, 2 interactions with chain 6 Hydrophobic interactions: 1:F.31, 1:V.34, 1:A.38, 1:A.41, 1:V.42, 1:W.45, 6:F.49, 6:F.49 SPO.65: 11 residues within 4Å: Chain 0: F.17 Chain 1: F.49 Chain 2: F.31, V.34, A.38, A.41, V.42, W.45 Ligands: BCL.61, SPO.62, BCL.63 8 PLIP interactions: 5 interactions with chain 2, 3 interactions with chain 1 Hydrophobic interactions: 2:F.31, 2:V.34, 2:A.41, 2:V.42, 2:W.45, 1:F.49, 1:F.49, 1:F.49 SPO.68: 20 residues within 4Å: Chain 0: F.25, H.32 Chain 1: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain 3: F.17, Q.20, F.23, L.24, L.27 Chain 4: K.6, I.7, V.10 Ligands: BCL.61, BCL.63, SPO.64 18 PLIP interactions: 7 interactions with chain 1, 4 interactions with chain 4, 5 interactions with chain 3, 2 interactions with chain 0 Hydrophobic interactions: 1:L.20, 1:V.23, 1:Y.24, 1:Y.24, 1:L.28, 1:F.31, 1:F.31, 4:K.6, 4:K.6, 4:I.7, 4:V.10, 3:F.17, 3:F.17, 3:F.23, 3:L.24, 3:L.27, 0:F.25, 0:H.32 SPO.71: 12 residues within 4Å: Chain 4: Q.20 Chain 5: F.49 Chain 6: F.31, V.34, A.38, A.41, V.42, W.45 Ligands: BCL.69, BCL.72, SPO.73, SPO.75 8 PLIP interactions: 5 interactions with chain 6, 3 interactions with chain 5 Hydrophobic interactions: 6:F.31, 6:A.38, 6:A.41, 6:V.42, 6:W.45, 5:F.49, 5:F.49, 5:F.49 SPO.73: 21 residues within 4Å: Chain 3: F.25, H.32, L.33 Chain 4: Q.20, F.23, L.24, L.27 Chain 6: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain 7: K.6, I.7, V.10 Ligands: SPO.64, BCL.67, BCL.70, SPO.71 19 PLIP interactions: 8 interactions with chain 6, 4 interactions with chain 7, 2 interactions with chain 3, 5 interactions with chain 4 Hydrophobic interactions: 6:E.19, 6:L.20, 6:L.20, 6:V.23, 6:V.23, 6:Y.24, 6:Y.24, 6:F.31, 7:K.6, 7:K.6, 7:I.7, 7:V.10, 3:F.25, 3:H.32, 4:F.23, 4:L.24, 4:L.24, 4:L.27, 4:L.27 SPO.75: 23 residues within 4Å: Chain 4: F.25, H.32, L.33 Chain 5: E.19, L.20, V.23, Y.24, G.27, L.28, F.31 Chain 7: F.17, Q.20, F.23, L.24, L.27 Chain B: K.6, I.7, V.10 Chain F: L.7 Ligands: SPO.13, BCL.69, SPO.71, BCL.72 21 PLIP interactions: 8 interactions with chain 5, 4 interactions with chain B, 1 interactions with chain F, 7 interactions with chain 7, 1 interactions with chain 4 Hydrophobic interactions: 5:E.19, 5:L.20, 5:V.23, 5:V.23, 5:V.23, 5:Y.24, 5:Y.24, 5:F.31, B:K.6, B:K.6, B:I.7, B:V.10, F:L.7, 7:F.17, 7:F.17, 7:F.23, 7:F.23, 7:L.24, 7:L.24, 7:L.27, 4:F.25

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.15: 30 residues within 4Å: Chain H: T.39, F.42, A.43, G.46, I.50, A.94, F.98, W.101, E.105, I.118, A.121, F.122, A.125, F.147, Y.149, G.150, I.151, H.154, L.239, V.242 Chain I: Y.209, A.212, L.213, A.216, M.217, W.251, M.255 Ligands: BCL.14, BCL.20, U10.22 14 PLIP interactions: 10 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:A.43, H:I.50, H:A.94, H:A.121, H:F.122, H:F.122, H:F.147, H:Y.149, H:L.239, H:V.242, I:Y.209, I:A.212, I:L.213, I:A.216 BPH.27: 24 residues within 4Å: Chain H: F.182, A.185, W.186, A.189, M.190, L.220, M.221 Chain I: S.59, L.60, G.63, A.64, F.67, F.68, S.124, W.128, V.132, M.145, A.148, F.149, A.152, A.272, T.276 Ligands: BCL.24, BCL.26 13 PLIP interactions: 9 interactions with chain I, 4 interactions with chain H Hydrophobic interactions: I:L.60, I:F.67, I:F.67, I:F.68, I:W.128, I:A.148, I:F.149, I:F.149, I:T.276, H:F.182, H:A.185, H:A.189 pi-Stacking: H:W.186

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

U10.16: 20 residues within 4Å: Chain H: 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, L.237 Ligands: U10.17, BCL.24 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:L.180, H:W.186, H:M.190, H:L.194, H:F.217, H:F.217, H:F.217, H:Y.223, H:V.225, H:V.225, H:I.230, H:I.230, H:L.233, H:L.237 Hydrogen bonds: H:V.225, H:G.226 U10.17: 10 residues within 4Å: Chain H: P.172, M.175, L.176, S.179, W.264 Chain I: F.90, I.178, F.179 Ligands: U10.16, BCL.24 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:M.175 U10.18: 9 residues within 4Å: Chain H: W.264, W.267 Chain I: M.86, R.87, D.88, L.89, F.90, F.91, F.179 8 PLIP interactions: 4 interactions with chain I, 4 interactions with chain H Hydrophobic interactions: I:L.89, I:F.90, H:W.267, H:W.267 Hydrogen bonds: I:L.89, I:F.90 pi-Stacking: H:W.267, H:W.267 U10.22: 26 residues within 4Å: Chain H: F.30, Y.31, V.32, G.36, I.40, W.101, R.104 Chain I: 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.14, BPH.15, 3PE.19, 3PE.30 17 PLIP interactions: 10 interactions with chain I, 7 interactions with chain H Hydrophobic interactions: I:M.217, I:W.251, I:F.257, I:F.257, I:A.259, I:I.264, I:W.267, I:W.267, H:F.30, H:F.30, H:F.30, H:V.32, H:I.40, H:I.40, H:W.101 Hydrogen bonds: I:T.221, I:A.259

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

3PE.19: 12 residues within 4Å: Chain H: P.29, F.30 Chain J: N.52, G.54, P.55, F.56 Chain K: R.15 Ligands: BCL.14, U10.22, 3PE.30, 3PE.33, 3PE.34 6 PLIP interactions: 4 interactions with chain J, 2 interactions with chain K Hydrophobic interactions: J:F.56, J:F.56 Hydrogen bonds: J:N.52, J:G.54 Salt bridges: K:R.15, K:R.15 3PE.25: 15 residues within 4Å: Chain H: N.200, P.201 Chain I: G.142, H.144, W.147, S.151, W.154, R.266, W.270, V.273, L.277 Chain J: S.19, F.20, F.23, Y.30 17 PLIP interactions: 12 interactions with chain I, 4 interactions with chain J, 1 interactions with chain H Hydrophobic interactions: I:W.147, I:W.154, I:W.154, I:W.154, I:W.154, I:W.270, I:V.273, I:L.277, I:L.277, J:F.23, J:F.23, J:F.23, J:Y.30 Salt bridges: I:H.144, I:H.144, I:R.266 Hydrogen bonds: H:N.200 3PE.28: 24 residues within 4Å: Chain I: A.61, A.65, F.68, T.69, V.72, W.73, W.75, Y.76, F.80, L.108, K.109, V.113 Chain V: V.29, L.33 Chain W: F.25, L.26, V.29, L.30, L.33, I.34, L.36, S.37, T.45 Chain Z: L.30 23 PLIP interactions: 14 interactions with chain I, 8 interactions with chain W, 1 interactions with chain V Hydrophobic interactions: I:A.65, I:F.68, I:T.69, I:W.73, I:W.75, I:W.75, I:Y.76, I:Y.76, I:Y.76, I:F.80, I:V.113, W:F.25, W:V.29, W:L.30, W:L.33, W:L.33, W:L.33, W:I.34, V:L.33 Hydrogen bonds: I:K.109, W:N.42 Salt bridges: I:K.109, I:K.109 3PE.29: 16 residues within 4Å: Chain H: Q.63, W.152 Chain I: P.199, L.203, A.207, M.274, W.296, H.300, Y.302 Chain J: S.14, I.17, W.18, F.20, W.21 Ligands: BCL.20, 3PE.30 11 PLIP interactions: 4 interactions with chain J, 5 interactions with chain I, 2 interactions with chain H Hydrophobic interactions: J:W.18, J:F.20, I:L.203, I:A.207, I:M.274, I:Y.302, H:Q.63, H:W.152 Hydrogen bonds: J:S.14, J:S.14 Salt bridges: I:H.300 3PE.30: 22 residues within 4Å: Chain H: F.30 Chain I: R.252, M.255, G.256, F.257, W.267, W.270, M.271 Chain J: L.27, I.28, L.31, Q.32, M.36, Y.40, Q.53, G.54, P.55, F.56 Ligands: 3PE.19, BCL.20, U10.22, 3PE.29 17 PLIP interactions: 8 interactions with chain I, 9 interactions with chain J Hydrophobic interactions: I:F.257, I:F.257, I:F.257, I:W.267, I:W.267, I:W.270, I:M.271, J:L.27, J:I.28, J:L.31, J:Q.32, J:F.56 Salt bridges: I:R.252 Hydrogen bonds: J:Q.32, J:Y.40, J:Q.53, J:F.56 3PE.33: 16 residues within 4Å: Chain D: R.15, V.16 Chain H: V.27, G.28 Chain J: N.52, E.97 Chain K: D.12, R.14, R.15, V.18, A.19, G.21, V.22 Ligands: 3PE.19, BCL.31, 3PE.34 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain K Hydrophobic interactions: D:R.15, D:V.16, K:R.15, K:V.18, K:A.19, K:V.22 Salt bridges: D:R.15, K:R.14, K:R.15 Hydrogen bonds: K:D.12 3PE.34: 16 residues within 4Å: Chain B: R.14, V.18, G.21, V.22 Chain J: N.52, Q.53, G.54 Chain K: F.11, R.15, V.16, A.19, V.22, F.23 Ligands: BCL.2, 3PE.19, 3PE.33 9 PLIP interactions: 1 interactions with chain B, 3 interactions with chain J, 5 interactions with chain K Hydrophobic interactions: B:V.18, K:V.22, K:F.23, K:F.23 Hydrogen bonds: J:Q.53, J:G.54, J:G.54 Salt bridges: K:R.15, K:R.15

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

FE.21: 5 residues within 4Å: Chain H: H.191, H.231 Chain I: H.218, E.233, H.265 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain I Metal complexes: H:H.191, H:H.231, I:H.218, I:E.233, I:H.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bracun, L. et al., Cryo-EM structure of a monomeric RC-LH1-PufX supercomplex with high-carotenoid content from Rhodobacter capsulatus. Structure (2023)

Release Date

2023-02-01

Peptides

Light-harvesting protein B-870 alpha chain: ABDKMPRSVWZ0347
LH1 beta chain: CEFLNOQTUXY1256
Intrinsic membrane protein PufX: G
Reaction center protein L chain: H
Reaction center protein M chain: I
Reaction center protein H chain: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
e

D
b

K
d

M
t

P
s

R
u

S
r

V
o

W
n

Z
k

0
j

3
i

4
g

7
f

C
D

E
A

F
E

L
B

N
S

O
T

Q
U

T
O

U
R

X
K

Y
N

1
I

2
J

5
F

6
G

G
X

H
L

I
M

J
H

Membrane

We predict this structure to be a membrane protein.
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Light-harvesting protein B-870 alpha chain

LH1 beta chain

Intrinsic membrane protein PufX

Reaction center protein L chain

Reaction center protein M chain

Reaction center protein H chain

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