SMTL ID : 5yq7.1

Cryo-EM structure of the RC-LH core complex from Roseiflexus castenholzii

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

BCL.1: 13 residues within 4Å: Chain A: G.36, L.37, H.44, W.53 Chain Z: I.26, H.27, F.36 Ligands: BCL.3, BCL.29, KGD.54, BCL.56, KGD.57, BCL.58 5 PLIP interactions: 2 interactions with chain Z, 3 interactions with chain A, Hydrophobic interactions: Z:I.26, Z:F.36, A:W.53 pi-Stacking: A:W.53 Metal complexes: A:H.44 BCL.2: 11 residues within 4Å: Chain A: W.14, H.26, V.29, V.30, I.33, Y.34 Chain B: A.43 Chain Z: S.11 Ligands: BCL.3, BCL.58, KGD.59 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:A.43, A:W.14, A:V.30 Metal complexes: A:H.26 BCL.3: 16 residues within 4Å: Chain 0: A.23, H.27, F.36 Chain A: I.33 Chain B: G.36, L.37, A.40, H.44, C.47, W.53 Ligands: BCL.1, BCL.2, BCL.4, KGD.57, BCL.58, BCL.61 10 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B, 2 interactions with chain 0, Hydrophobic interactions: A:I.33, B:W.53, B:W.53, B:W.53, B:W.53, 0:F.36, 0:F.36 pi-Stacking: B:W.53, B:W.53 Metal complexes: B:H.44 BCL.4: 15 residues within 4Å: Chain 0: F.8, S.11 Chain B: W.14, H.26, V.29, V.30, I.33, Y.34, L.37 Chain C: L.24, I.39 Ligands: BCL.3, BCL.5, KGD.60, BCL.61 9 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C, 1 interactions with chain 0, Hydrophobic interactions: B:W.14, B:V.30, B:V.30, B:L.37, C:L.24, C:I.39, 0:F.8 pi-Stacking: B:H.26 Metal complexes: B:H.26 BCL.5: 15 residues within 4Å: Chain 1: A.23, I.26, H.27, F.36 Chain C: I.33, G.36, L.37, A.40, H.44, C.47, W.53 Ligands: BCL.4, KGD.59, BCL.61, BCL.62 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain 1, Hydrophobic interactions: C:I.33, C:W.53, C:W.53, C:W.53, C:W.53, 1:I.26, 1:F.36 pi-Stacking: C:W.53, C:W.53 Metal complexes: C:H.44 BCL.6: 15 residues within 4Å: Chain 1: F.8, S.11 Chain C: P.11, W.14, H.26, V.29, V.30, I.33, Y.34 Chain E: L.24, A.43 Ligands: BCL.12, KGD.60, BCL.62, KGD.63 7 PLIP interactions: 2 interactions with chain E, 1 interactions with chain 1, 4 interactions with chain C, Hydrophobic interactions: E:L.24, E:A.43, 1:F.8, C:P.11, C:W.14, C:V.30 Metal complexes: C:H.26 BCL.7: 14 residues within 4Å: Chain 8: M.191, I.194, F.195, L.198, G.199, L.202 Chain D: W.167, F.185, H.192, L.193, V.196 Ligands: BCL.8, BPH.9, BCL.70 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain 8, Hydrophobic interactions: D:W.167, D:F.185, D:L.193, D:V.196, 8:I.194, 8:F.195, 8:L.202 Metal complexes: D:H.192 BCL.8: 18 residues within 4Å: Chain 8: Y.185 Chain D: F.136, V.163, L.170, I.199, G.200, F.206, F.207, H.212, I.216, V.275, S.278, N.279, I.282 Ligands: BCL.7, BPH.9, BCL.70, BPH.71 8 PLIP interactions: 8 interactions with chain D, Hydrophobic interactions: D:F.136, D:I.199, D:F.206, D:F.206, D:F.207, D:I.216, D:I.282 Metal complexes: D:H.212 BCL.12: 15 residues within 4Å: Chain 2: A.23, I.26, H.27, F.36 Chain E: G.36, L.37, H.44, W.53 Ligands: BCL.6, BCL.13, BCL.14, KGD.60, BCL.62, KGD.63, BCL.64 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain 2, Hydrophobic interactions: E:W.53, E:W.53, 2:I.26, 2:F.36 Metal complexes: E:H.44 BCL.13: 13 residues within 4Å: Chain 2: F.8 Chain E: P.11, W.14, H.26, V.29, V.30, I.33 Chain F: I.39, A.43 Ligands: BCL.12, BCL.14, BCL.64, KGD.65 7 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E, 2 interactions with chain 2, Hydrophobic interactions: F:I.39, F:A.43, E:P.11, 2:F.8, 2:F.8 Salt bridges: E:H.26 Metal complexes: E:H.26 BCL.14: 14 residues within 4Å: Chain 3: A.23, I.26, H.27 Chain E: L.37 Chain F: L.37, H.44, W.53 Ligands: BCL.12, BCL.13, BCL.15, KGD.63, BCL.64, KGD.65, BCL.66 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, Metal complexes: F:H.44 Hydrophobic interactions: E:L.37 BCL.15: 13 residues within 4Å: Chain 3: E.7, F.8, S.11 Chain F: W.14, H.26, V.29, V.30, I.33, Y.34 Chain G: I.39 Ligands: BCL.14, BCL.16, KGD.67 5 PLIP interactions: 1 interactions with chain 3, 3 interactions with chain F, 1 interactions with chain G, Hydrophobic interactions: 3:F.8, F:W.14, G:I.39 Salt bridges: F:H.26 Metal complexes: F:H.26 BCL.16: 13 residues within 4Å: Chain 4: A.23, I.26, H.27, V.30 Chain G: G.36, H.44, C.47, W.53 Ligands: BCL.15, KGD.65, BCL.66, KGD.67, BCL.68 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain 4, Hydrophobic interactions: G:W.53, 4:V.30 Metal complexes: G:H.44 BCL.17: 9 residues within 4Å: Chain 4: S.11 Chain G: W.14, H.26, V.29, V.30, I.33, Y.34 Ligands: BCL.18, BCL.68 3 PLIP interactions: 3 interactions with chain G, Hydrophobic interactions: G:W.14, G:V.30 Metal complexes: G:H.26 BCL.18: 12 residues within 4Å: Chain 5: M.22, A.23, I.26, H.27 Chain H: G.36, H.44, W.53 Chain J: W.41, I.42 Ligands: BCL.17, KGD.67, BCL.68 8 PLIP interactions: 5 interactions with chain H, 2 interactions with chain J, 1 interactions with chain 5, Hydrophobic interactions: H:W.53, H:W.53, H:W.53, J:W.41, J:I.42, 5:I.26 pi-Stacking: H:W.53 Metal complexes: H:H.44 BCL.19: 8 residues within 4Å: Chain 5: S.11 Chain H: W.14, H.26, V.29, V.30, I.33, Y.34, L.37 4 PLIP interactions: 4 interactions with chain H, Hydrophobic interactions: H:W.14, H:L.37 Salt bridges: H:H.26 Metal complexes: H:H.26 BCL.20: 14 residues within 4Å: Chain I: G.36, L.37, H.44, C.47, W.53 Chain W: A.23, I.26, H.27, F.36 Ligands: BCL.41, BCL.42, KGD.48, BCL.51, BCL.52 7 PLIP interactions: 5 interactions with chain I, 2 interactions with chain W, Hydrophobic interactions: I:W.53, I:W.53, I:W.53, W:I.26, W:F.36 pi-Stacking: I:W.53 Metal complexes: I:H.44 BCL.21: 10 residues within 4Å: Chain I: P.11, W.14, H.26, V.29, V.30, I.33 Chain W: F.8, S.11 Ligands: BCL.26, KGD.53 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain W, Hydrophobic interactions: I:W.14, I:V.30, W:F.8 Metal complexes: I:H.26 BCL.26: 14 residues within 4Å: Chain K: G.36, H.44, C.47, W.53 Chain X: A.23, I.26, H.27, V.30 Ligands: BCL.21, BCL.28, KGD.50, BCL.52, KGD.53, BCL.55 6 PLIP interactions: 2 interactions with chain X, 4 interactions with chain K, Hydrophobic interactions: X:I.26, X:V.30, K:W.53, K:W.53, K:W.53 Metal complexes: K:H.44 BCL.27: 11 residues within 4Å: Chain K: P.11, W.14, H.26, V.29, V.30, I.33, L.37 Chain L: A.43 Chain X: S.11 Ligands: BCL.28, KGD.54 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L, Hydrophobic interactions: K:W.14, K:V.30, K:L.37, L:A.43 Metal complexes: K:H.26 BCL.28: 15 residues within 4Å: Chain L: I.33, G.36, L.37, H.44, C.47, W.53 Chain Y: A.23, H.27 Ligands: BCL.26, BCL.27, BCL.29, KGD.53, KGD.54, BCL.55, BCL.56 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain Y, Hydrophobic interactions: L:I.33, L:W.53, Y:H.27 pi-Stacking: L:W.53 Metal complexes: L:H.44, L:H.44 BCL.29: 11 residues within 4Å: Chain L: W.14, H.26, V.29, V.30, I.33 Chain Y: F.8, S.11 Ligands: BCL.1, BCL.28, KGD.54, KGD.57 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain Y, Hydrophobic interactions: L:W.14, L:V.30, Y:F.8, Y:F.8 Metal complexes: L:H.26 BCL.30: 16 residues within 4Å: Chain 7: X.9 Chain M: G.36, L.37, A.40, H.44, W.53 Chain O: W.38 Chain S: A.23, I.26, H.27, V.30 Ligands: BCL.31, BCL.32, KGD.34, BCL.36, BCL.43 8 PLIP interactions: 3 interactions with chain S, 4 interactions with chain M, 1 interactions with chain O, Hydrophobic interactions: S:I.26, S:H.27, S:V.30, M:W.53, M:W.53, M:W.53, O:W.38 Metal complexes: M:H.44 BCL.31: 12 residues within 4Å: Chain M: W.14, H.26, V.29, V.30, I.33 Chain N: L.24, I.39, A.43 Chain S: F.6 Ligands: BCL.30, BCL.32, KGD.35 8 PLIP interactions: 3 interactions with chain N, 1 interactions with chain S, 4 interactions with chain M, Hydrophobic interactions: N:L.24, N:I.39, N:A.43, S:F.6, M:W.14, M:W.14, M:V.30 Metal complexes: M:H.26 BCL.32: 15 residues within 4Å: Chain N: T.32, G.36, L.37, A.40, H.44, W.53 Chain O: A.23, I.26, H.27, F.36 Ligands: BCL.30, BCL.31, KGD.34, BCL.36, BCL.45 10 PLIP interactions: 7 interactions with chain N, 3 interactions with chain O, Hydrophobic interactions: N:T.32, N:A.40, N:W.53, N:W.53, N:W.53, O:I.26, O:F.36 pi-Stacking: N:W.53 Metal complexes: N:H.44 Hydrogen bonds: O:H.27 BCL.33: 10 residues within 4Å: Chain N: P.11, W.14, H.26, V.29, V.30, I.33 Chain O: F.8, S.11 Ligands: BCL.37, KGD.44 4 PLIP interactions: 1 interactions with chain O, 3 interactions with chain N, Hydrophobic interactions: O:F.8, N:W.14 Salt bridges: N:H.26 Metal complexes: N:H.26 BCL.36: 13 residues within 4Å: Chain D: F.55 Chain N: A.40, H.44 Chain O: V.13, T.16, L.20, H.27, W.38 Chain S: V.14 Ligands: BCL.30, BCL.32, KGD.34, KGD.35 7 PLIP interactions: 5 interactions with chain O, 1 interactions with chain S, 1 interactions with chain D, Hydrophobic interactions: O:L.20, O:W.38, O:W.38, O:W.38, S:V.14, D:F.55 Metal complexes: O:H.27 BCL.37: 14 residues within 4Å: Chain N: I.33 Chain P: G.36, L.37, H.44, C.47, W.53 Chain T: A.23, I.26, H.27 Ligands: BCL.33, KGD.35, KGD.44, BCL.45, BCL.46 7 PLIP interactions: 3 interactions with chain T, 4 interactions with chain P, Hydrophobic interactions: T:I.26, T:I.26, P:W.53, P:W.53, P:W.53 Hydrogen bonds: T:H.27 Metal complexes: P:H.44 BCL.38: 12 residues within 4Å: Chain P: W.14, H.26, V.29, V.30, I.33, Y.34 Chain Q: A.43 Chain T: S.11 Ligands: BCL.39, KGD.44, BCL.46, KGD.47 3 PLIP interactions: 2 interactions with chain P, 1 interactions with chain Q, Hydrophobic interactions: P:W.14, Q:A.43 Metal complexes: P:H.26 BCL.39: 14 residues within 4Å: Chain Q: T.32, G.36, L.37, H.44, C.47, W.53 Chain U: A.23, I.26, H.27 Ligands: BCL.38, BCL.41, KGD.44, BCL.46, BCL.49 7 PLIP interactions: 6 interactions with chain Q, 1 interactions with chain U, Hydrophobic interactions: Q:T.32, Q:W.53, Q:W.53, Q:W.53, U:I.26 Metal complexes: Q:H.44, Q:H.44 BCL.40: 14 residues within 4Å: Chain Q: P.11, W.14, H.26, V.29, V.30, I.33, L.37 Chain R: I.39 Chain U: E.7, F.8, S.11 Ligands: BCL.41, KGD.48, BCL.49 6 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain R, 1 interactions with chain U, Hydrophobic interactions: Q:P.11, Q:L.37, R:I.39, U:F.8 Salt bridges: Q:H.26 Metal complexes: Q:H.26 BCL.41: 17 residues within 4Å: Chain Q: I.33 Chain R: G.36, L.37, H.44, C.47, W.53 Chain V: A.23, I.26, H.27, F.36 Ligands: BCL.20, BCL.39, BCL.40, KGD.47, KGD.48, BCL.49, BCL.51 8 PLIP interactions: 2 interactions with chain V, 5 interactions with chain R, 1 interactions with chain Q, Hydrophobic interactions: V:I.26, V:F.36, R:W.53, R:W.53, R:W.53, Q:I.33 pi-Stacking: R:W.53 Metal complexes: R:H.44 BCL.42: 10 residues within 4Å: Chain I: L.24 Chain R: P.11, W.14, H.26, V.30, I.33 Chain V: F.8 Ligands: BCL.20, KGD.50, BCL.51 6 PLIP interactions: 4 interactions with chain R, 1 interactions with chain I, 1 interactions with chain V, Hydrophobic interactions: R:P.11, R:W.14, R:W.14, I:L.24, V:F.8 Metal complexes: R:H.26 BCL.43: 8 residues within 4Å: Chain 7: X.17, X.20 Chain M: H.44 Chain S: T.16, H.27, W.38 Ligands: BCL.30, KGD.34 4 PLIP interactions: 4 interactions with chain S, Hydrophobic interactions: S:W.38, S:W.38, S:W.38 Metal complexes: S:H.27 BCL.45: 17 residues within 4Å: Chain D: A.74, I.78 Chain N: W.53 Chain O: L.18 Chain P: G.36, A.40, H.44 Chain T: T.16, L.20, A.23, H.27, V.30, W.38 Ligands: BCL.32, KGD.35, BCL.37, KGD.44 8 PLIP interactions: 6 interactions with chain T, 2 interactions with chain D, Hydrophobic interactions: T:T.16, T:L.20, T:V.30, T:W.38, T:W.38, D:A.74, D:I.78 Metal complexes: T:H.27 BCL.46: 14 residues within 4Å: Chain Q: A.40, H.44, C.47 Chain T: F.6 Chain U: T.16, L.20, A.23, H.27, W.38 Ligands: BCL.37, BCL.38, BCL.39, KGD.44, KGD.47 5 PLIP interactions: 4 interactions with chain U, 1 interactions with chain T, Hydrophobic interactions: U:T.16, U:L.20, U:W.38, T:F.6 Metal complexes: U:H.27 BCL.49: 15 residues within 4Å: Chain Q: W.53 Chain R: I.39, H.44 Chain U: F.6, S.15 Chain V: V.13, L.20, A.23, H.27, W.38 Ligands: BCL.39, BCL.40, BCL.41, KGD.47, KGD.48 5 PLIP interactions: 2 interactions with chain V, 2 interactions with chain U, 1 interactions with chain Q, Hydrophobic interactions: V:L.20, U:F.6, U:F.6, Q:W.53 Metal complexes: V:H.27 BCL.51: 14 residues within 4Å: Chain I: I.39, A.40, H.44 Chain V: V.14 Chain W: V.13, L.20, A.23, H.27, W.38 Ligands: BCL.20, BCL.41, BCL.42, KGD.48, KGD.50 4 PLIP interactions: 3 interactions with chain W, 1 interactions with chain V, Hydrophobic interactions: W:V.13, W:L.20, V:V.14 Metal complexes: W:H.27 BCL.52: 14 residues within 4Å: Chain K: G.36, I.39, H.44 Chain X: V.13, T.16, L.20, A.23, H.27, F.36, W.38 Ligands: BCL.20, BCL.26, KGD.50, KGD.53 5 PLIP interactions: 5 interactions with chain X, Hydrophobic interactions: X:V.13, X:T.16, X:L.20, X:F.36 Metal complexes: X:H.27 BCL.55: 15 residues within 4Å: Chain L: A.40, A.43, H.44 Chain X: T.10, V.14, S.15 Chain Y: G.19, L.20, H.27, L.31, W.38 Ligands: BCL.26, BCL.28, KGD.53, KGD.54 6 PLIP interactions: 1 interactions with chain L, 4 interactions with chain Y, 1 interactions with chain X, Hydrophobic interactions: L:A.43, Y:L.31, Y:L.31, Y:W.38, X:T.10 Metal complexes: Y:H.27 BCL.56: 13 residues within 4Å: Chain A: A.40, H.44 Chain Y: V.14, I.26 Chain Z: T.16, L.20, H.27, L.31, W.38 Ligands: BCL.1, BCL.28, KGD.54, KGD.57 6 PLIP interactions: 5 interactions with chain Z, 1 interactions with chain Y, Hydrophobic interactions: Z:T.16, Z:L.20, Z:L.31, Z:L.31, Y:I.26 Metal complexes: Z:H.27 BCL.58: 17 residues within 4Å: Chain 0: V.13, T.16, L.20, A.23, H.27, L.31, F.36, W.38 Chain B: I.39, A.40, A.43, H.44 Ligands: BCL.1, BCL.2, BCL.3, KGD.57, KGD.59 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain 0, Hydrophobic interactions: B:A.43, 0:V.13, 0:T.16, 0:L.20, 0:F.36, 0:W.38, 0:W.38 Metal complexes: 0:H.27 BCL.61: 18 residues within 4Å: Chain 0: F.6, S.11, V.14, S.15 Chain 1: V.13, A.23, H.27, F.36, W.38 Chain C: I.39, A.40, H.44, C.47 Ligands: BCL.3, BCL.4, BCL.5, KGD.59, KGD.60 4 PLIP interactions: 3 interactions with chain 1, 1 interactions with chain 0, Hydrophobic interactions: 1:V.13, 1:F.36, 0:F.6 Metal complexes: 1:H.27 BCL.62: 15 residues within 4Å: Chain 1: V.14 Chain 2: V.13, T.16, H.27, W.38 Chain C: W.53 Chain E: A.40, A.43, H.44, C.47 Ligands: BCL.5, BCL.6, BCL.12, KGD.60, KGD.63 6 PLIP interactions: 4 interactions with chain 2, 1 interactions with chain E, 1 interactions with chain 1, Hydrophobic interactions: 2:T.16, 2:W.38, E:A.43, 1:V.14 pi-Stacking: 2:W.38 Metal complexes: 2:H.27 BCL.64: 16 residues within 4Å: Chain 2: V.14 Chain 3: V.13, T.16, L.20, A.23, H.27, V.30, W.38 Chain F: I.39, A.40, H.44 Ligands: BCL.12, BCL.13, BCL.14, KGD.63, KGD.65 6 PLIP interactions: 1 interactions with chain 2, 5 interactions with chain 3, Hydrophobic interactions: 2:V.14, 3:V.13, 3:V.13, 3:L.20, 3:V.30 Metal complexes: 3:H.27 BCL.66: 14 residues within 4Å: Chain 3: F.6, V.14 Chain 4: T.16, L.20, A.23, H.27, W.38 Chain G: A.40, A.43, H.44 Ligands: BCL.14, BCL.16, KGD.65, KGD.67 5 PLIP interactions: 2 interactions with chain 3, 2 interactions with chain 4, 1 interactions with chain G, Hydrophobic interactions: 3:F.6, 3:V.14, 4:L.20, G:A.43 Metal complexes: 4:H.27 BCL.68: 16 residues within 4Å: Chain 4: S.11, S.15 Chain 5: T.16, L.20, A.23, H.27, W.38 Chain H: I.39, A.40, A.43, H.44, C.47 Ligands: BCL.16, BCL.17, BCL.18, KGD.67 4 PLIP interactions: 4 interactions with chain 5, Hydrophobic interactions: 5:L.20, 5:W.38 pi-Stacking: 5:W.38 Metal complexes: 5:H.27 BCL.70: 17 residues within 4Å: Chain 8: F.51, L.144, S.178, F.184, Y.185, H.190, S.193, I.194, L.197, G.268, L.272 Chain D: Y.201, F.220 Ligands: BCL.7, BCL.8, BPH.71, BPH.72 6 PLIP interactions: 6 interactions with chain 8, Hydrophobic interactions: 8:F.184, 8:Y.185, 8:I.194, 8:L.197 Hydrogen bonds: 8:Y.185 Metal complexes: 8:H.190

3 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.9: 19 residues within 4Å: Chain 8: L.198, T.201, L.202, M.206, W.240 Chain D: I.80, V.84, W.139, Q.143, V.156, A.159, F.160, L.187, G.188, I.189, G.271, V.275 Ligands: BCL.7, BCL.8 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain 8 Hydrophobic interactions: D:I.80, D:I.80, D:V.84, D:W.139, D:A.159, D:F.160, D:F.160, D:L.187, D:L.187, D:I.189, D:V.275, 8:L.202 Hydrogen bonds: D:Q.143 BPH.71: 13 residues within 4Å: Chain 8: L.110, I.148, Y.149, F.167, R.168, I.170, L.171 Chain D: A.213, I.216, T.217 Ligands: BCL.8, BCL.70, BPH.72 5 PLIP interactions: 4 interactions with chain 8, 1 interactions with chain D Hydrophobic interactions: 8:L.110, 8:F.167, D:T.217 Hydrogen bonds: 8:Y.149 Salt bridges: 8:R.168 BPH.72: 13 residues within 4Å: Chain 8: F.51, W.117, F.138, A.141, A.265 Chain D: F.220, T.223, L.224, H.227, M.228, L.254 Ligands: BCL.70, BPH.71 13 PLIP interactions: 10 interactions with chain 8, 3 interactions with chain D Hydrophobic interactions: 8:F.51, 8:F.51, 8:W.117, 8:W.117, 8:F.138, 8:F.138, 8:F.138, 8:F.138, 8:A.141, 8:A.265, D:T.223, D:L.224, D:L.254

2 x MQE: 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione(Covalent)(Non-covalent)

MQE.10: 13 residues within 4Å: Chain 6: X.11, X.14 Chain D: F.225, H.247, W.250, S.257, I.258, G.259, E.260, I.261, I.263, V.266, W.269 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.225, D:W.250, D:I.258, D:I.263, D:I.263, D:V.266, D:W.269 Hydrogen bonds: D:G.259 MQE.69: 18 residues within 4Å: Chain 8: M.206, H.207, T.210, W.240, W.246, A.248, N.249, I.253 Chain D: F.67, I.77, I.81, V.84, L.88, R.142 Chain U: L.17, V.21, L.24, L.25 14 PLIP interactions: 6 interactions with chain 8, 5 interactions with chain D, 3 interactions with chain U Hydrophobic interactions: 8:M.206, 8:W.240, 8:W.246, 8:A.248, 8:I.253, D:I.77, D:I.77, D:I.81, D:V.84, D:L.88, U:L.17, U:V.21, U:L.25 Hydrogen bonds: 8:H.207

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

FE.11: 5 residues within 4Å: Chain 8: H.207, E.222, H.254 Chain D: H.229, H.264 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain 8 Metal complexes: D:H.229, 8:H.207, 8:E.222, 8:E.222, 8:H.254

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)

HEM.22: 13 residues within 4Å: Chain J: Q.83, V.91, V.93, L.94, M.106, V.107, V.110, C.118, C.121, H.122, N.126, A.128, R.143 14 PLIP interactions: 14 interactions with chain J, Hydrophobic interactions: J:Q.83, J:V.91, J:V.91, J:V.93, J:V.93, J:V.107, J:V.110, J:C.118, J:R.143 Hydrogen bonds: J:N.126, J:A.128 Salt bridges: J:R.143 pi-Stacking: J:H.122 Metal complexes: J:H.122 HEM.23: 13 residues within 4Å: Chain J: Y.120, M.145, M.146, M.148, C.171, T.173, C.174, H.175, G.181, L.182, I.285, M.286 Ligands: HEM.25 9 PLIP interactions: 9 interactions with chain J, Hydrophobic interactions: J:I.285, J:M.286 Hydrogen bonds: J:Y.120, J:Y.120, J:G.181, J:L.182 pi-Stacking: J:H.175, J:H.175 Metal complexes: J:H.175 HEM.24: 18 residues within 4Å: Chain 8: I.179 Chain D: Y.204 Chain J: Y.205, G.207, G.208, L.209, V.210, V.211, T.212, N.225, Q.226, M.229, C.240, C.243, H.244, P.250, S.260, I.261 13 PLIP interactions: 11 interactions with chain J, 1 interactions with chain D, 1 interactions with chain 8, Hydrophobic interactions: J:T.212, J:M.229, J:C.240, J:I.261, D:Y.204, 8:I.179 Hydrogen bonds: J:G.207, J:G.208, J:L.209, J:T.212, J:T.212 pi-Stacking: J:H.244 Metal complexes: J:H.244 HEM.25: 15 residues within 4Å: Chain J: G.165, G.166, Y.167, I.169, C.174, M.232, Q.256, H.259, M.263, S.292, C.293, H.297, N.301, I.302 Ligands: HEM.23 11 PLIP interactions: 11 interactions with chain J, Hydrophobic interactions: J:I.169, J:C.293, J:I.302, J:I.302 Hydrogen bonds: J:Y.167, J:Y.167, J:Q.256, J:N.301 pi-Stacking: J:H.297, J:H.297 Metal complexes: J:H.297

14 x KGD: beta,psi-caroten-4-one(Non-covalent)(Covalent)

KGD.34: 12 residues within 4Å: Chain M: V.25, V.29, I.33 Chain O: H.27 Chain S: T.16, G.19, M.22, I.26 Ligands: BCL.30, BCL.32, BCL.36, BCL.43 5 PLIP interactions: 2 interactions with chain S, 2 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: S:M.22, S:I.26, M:V.25, M:I.33, O:H.27 KGD.35: 13 residues within 4Å: Chain N: V.29, I.33 Chain O: S.15, T.16, G.19, M.22, I.26 Chain T: L.24, H.27 Ligands: BCL.31, BCL.36, BCL.37, BCL.45 6 PLIP interactions: 2 interactions with chain N, 2 interactions with chain T, 2 interactions with chain O Hydrophobic interactions: N:V.29, N:I.33, T:L.24, T:H.27, O:M.22, O:I.26 KGD.44: 18 residues within 4Å: Chain O: S.11 Chain P: I.28, V.29 Chain T: S.15, T.16, L.18, G.19, L.20, M.22 Chain U: L.20, L.24, H.27 Ligands: BCL.33, BCL.37, BCL.38, BCL.39, BCL.45, BCL.46 6 PLIP interactions: 2 interactions with chain P, 3 interactions with chain U, 1 interactions with chain T Hydrophobic interactions: P:I.28, P:V.29, U:L.20, U:L.24, U:H.27, T:M.22 KGD.47: 12 residues within 4Å: Chain Q: I.28, V.29 Chain T: S.11 Chain U: T.16, G.19, M.22 Chain V: L.24, H.27 Ligands: BCL.38, BCL.41, BCL.46, BCL.49 5 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain V, 1 interactions with chain U Hydrophobic interactions: Q:I.28, Q:V.29, V:L.24, V:H.27, U:M.22 KGD.48: 17 residues within 4Å: Chain R: V.29, I.33 Chain V: S.15, T.16, L.18, G.19, M.22, I.26 Chain W: L.24, H.27, F.28, L.31 Ligands: BCL.20, BCL.40, BCL.41, BCL.49, BCL.51 8 PLIP interactions: 3 interactions with chain V, 4 interactions with chain W, 1 interactions with chain R Hydrophobic interactions: V:L.18, V:M.22, V:I.26, W:L.24, W:H.27, W:F.28, W:L.31, R:I.33 KGD.50: 14 residues within 4Å: Chain I: I.28, V.29 Chain V: S.11 Chain W: S.15, T.16, L.18, G.19, M.22 Chain X: L.24, H.27 Ligands: BCL.26, BCL.42, BCL.51, BCL.52 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain X Hydrophobic interactions: I:I.28, I:V.29, X:L.24, X:H.27 KGD.53: 17 residues within 4Å: Chain K: I.28, I.33 Chain W: S.11 Chain X: S.15, T.16, L.18, G.19, L.20, M.22, I.26 Chain Y: L.24, H.27 Ligands: BCL.21, BCL.26, BCL.28, BCL.52, BCL.55 6 PLIP interactions: 2 interactions with chain K, 3 interactions with chain X, 1 interactions with chain Y Hydrophobic interactions: K:I.28, K:I.33, X:L.18, X:M.22, X:I.26, Y:H.27 KGD.54: 18 residues within 4Å: Chain L: I.28, V.29, I.33 Chain X: S.11 Chain Y: S.15, T.16, L.18, G.19, M.22, I.26 Chain Z: L.24, H.27 Ligands: BCL.1, BCL.27, BCL.28, BCL.29, BCL.55, BCL.56 7 PLIP interactions: 2 interactions with chain Y, 3 interactions with chain L, 2 interactions with chain Z Hydrophobic interactions: Y:M.22, Y:I.26, L:I.28, L:V.29, L:I.33, Z:L.24, Z:H.27 KGD.57: 18 residues within 4Å: Chain 0: L.24, H.27 Chain A: V.25, I.28, V.29, T.32, I.33 Chain Y: F.6 Chain Z: T.16, L.18, G.19, M.22, I.26 Ligands: BCL.1, BCL.3, BCL.29, BCL.56, BCL.58 10 PLIP interactions: 5 interactions with chain A, 2 interactions with chain Z, 2 interactions with chain 0, 1 interactions with chain Y Hydrophobic interactions: A:V.25, A:I.28, A:V.29, A:V.29, A:I.33, Z:L.18, Z:I.26, 0:L.24, 0:H.27, Y:F.6 KGD.59: 16 residues within 4Å: Chain 0: S.15, T.16, L.18, G.19, M.22, I.26 Chain 1: L.24, H.27 Chain B: V.29, I.33 Chain Z: F.6, S.11 Ligands: BCL.2, BCL.5, BCL.58, BCL.61 7 PLIP interactions: 2 interactions with chain B, 1 interactions with chain Z, 3 interactions with chain 0, 1 interactions with chain 1 Hydrophobic interactions: B:V.29, B:I.33, Z:F.6, 0:M.22, 0:I.26, 0:I.26, 1:H.27 KGD.60: 18 residues within 4Å: Chain 1: V.12, S.15, T.16, L.18, G.19, M.22, L.25, I.26 Chain 2: L.24, H.27, F.28 Chain C: V.29, I.33 Ligands: BCL.4, BCL.6, BCL.12, BCL.61, BCL.62 9 PLIP interactions: 4 interactions with chain 2, 1 interactions with chain C, 4 interactions with chain 1 Hydrophobic interactions: 2:L.24, 2:L.24, 2:H.27, 2:F.28, C:I.33, 1:V.12, 1:L.18, 1:L.25, 1:I.26 KGD.63: 17 residues within 4Å: Chain 2: V.12, S.15, T.16, L.18, G.19, M.22, L.25, I.26 Chain 3: H.27, F.28 Chain E: V.25, V.29 Ligands: BCL.6, BCL.12, BCL.14, BCL.62, BCL.64 8 PLIP interactions: 5 interactions with chain 2, 2 interactions with chain 3, 1 interactions with chain E Hydrophobic interactions: 2:V.12, 2:L.18, 2:L.25, 2:I.26, 2:I.26, 3:H.27, 3:F.28, E:V.25 KGD.65: 15 residues within 4Å: Chain 2: F.6, S.11 Chain 3: T.16, L.18, G.19, M.22 Chain 4: L.24, H.27 Chain F: V.29, I.33 Ligands: BCL.13, BCL.14, BCL.16, BCL.64, BCL.66 7 PLIP interactions: 2 interactions with chain 3, 1 interactions with chain 2, 2 interactions with chain 4, 2 interactions with chain F Hydrophobic interactions: 3:L.18, 3:M.22, 2:F.6, 4:L.24, 4:H.27, F:V.29, F:I.33 KGD.67: 20 residues within 4Å: Chain 3: S.11 Chain 4: S.15, T.16, L.18, G.19, L.20, M.22, L.25, I.26 Chain 5: A.23, L.24, H.27 Chain G: I.28, V.29, I.33 Ligands: BCL.15, BCL.16, BCL.18, BCL.66, BCL.68 9 PLIP interactions: 2 interactions with chain 5, 4 interactions with chain 4, 3 interactions with chain G Hydrophobic interactions: 5:L.24, 5:H.27, 4:L.18, 4:M.22, 4:L.25, 4:I.26, G:I.28, G:V.29, G:I.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xin, Y.Y. et al., Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote. Nat Commun (2018)

Release Date

2018-05-02

Peptides

Beta subunit of light-harvesting 1: ABCEFGHIKLMNPQR
Precursor for L subunits of photosynthetic reaction center: D
Cytochrome subunit of photosynthetic reaction center: J
Alpha subunit of light-harvesting 1: OSTUVWXYZ012345
Peptide from Precursor for L and M subunits of photosynthetic reaction center: 6
Subunit X: 7
Precursor for M subunits of photosynthetic reaction center: 8

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
B

C
0

E
8

F
6

G
4

H
2

I
K

K
I

L
G

M
W

N
U

P
S

Q
Q

R
O

D
L

J
C

O
T

S
V

T
R

U
P

V
N

W
J

X
H

Y
F

Z
D

0
A

1
9

2
7

3
5

4
3

5
1

6
Y

7
X

8
M

Membrane

We predict this structure to be a membrane protein.
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Beta subunit of light-harvesting 1

Precursor for L subunits of photosynthetic reaction center

Cytochrome subunit of photosynthetic reaction center

Alpha subunit of light-harvesting 1

Peptide from Precursor for L and M subunits of photosynthetic reaction center

Subunit X

Precursor for M subunits of photosynthetic reaction center

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