SMTL ID : 4ogq.1

Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome b6f Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-mer

Ligands

8 x HEC: HEME C(Non-covalent)(Covalent)

HEC.1: 23 residues within 4Å: Chain A: F.44, Q.47, F.48, G.51, F.52, M.54, Y.58, R.83, H.86, R.87, A.90, M.93, T.128, F.131, G.132, G.135, L.138, P.139, H.187, T.188, P.192 Chain B: E.78 Chain I: F.189 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.44, A:Q.47, A:F.48, A:M.54, A:Y.58, A:R.87, A:T.128, A:F.131, A:F.131, A:F.131, A:F.131, A:L.138, A:P.192 Water bridges: A:R.83 Salt bridges: A:R.83, A:R.83, A:R.87 Metal complexes: A:H.86, A:H.187 HEC.2: 28 residues within 4Å: Chain A: Y.34, G.37, G.38, T.40, L.41, M.93, M.97, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, V.122, L.124, A.125, T.128, M.199, H.202, F.203, I.206, G.210, I.211, S.212 Ligands: HEC.3 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:T.40, A:V.101, A:V.104, A:T.117, A:W.118, A:W.118, A:V.122, A:L.124, A:L.124, A:A.125, A:F.203, A:I.211 Hydrogen bonds: A:G.37, A:G.38, A:S.212 Water bridges: A:R.114 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 pi-Cation interactions: A:H.100 Metal complexes: A:H.100, A:H.202 HEC.3: 20 residues within 4Å: Chain A: V.30, N.31, Y.34, C.35, G.38, L.41, F.203, I.206, R.207, G.210, I.211 Chain B: N.25, F.40, V.43, I.44 Chain H: R.26 Ligands: HEC.2, 2WM.9, 8K6.11, UMQ.12 16 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.30, A:V.30, A:F.203, A:F.203, A:F.203, A:I.211, B:V.43, B:V.43, B:I.44 Hydrogen bonds: A:I.211, B:N.25 Water bridges: A:R.207, A:R.207 Salt bridges: A:R.207 pi-Stacking: B:F.40 Metal complexes: H2O.1 HEC.16: 20 residues within 4Å: Chain C: Y.45, P.46, W.48, A.49, C.66, C.69, H.70, Q.104, L.114, N.115, V.116, G.117, A.118, V.119, N.198, G.200, R.201, G.202, V.204, Y.205 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:Y.45, C:P.46, C:W.48, C:W.48, C:N.115, C:V.119, C:R.201, C:Y.205, C:Y.205 Hydrogen bonds: C:Q.104, C:N.115, C:N.115, C:N.115, C:G.200 Water bridges: C:Y.45, C:Y.45 Salt bridges: C:R.201 pi-Stacking: C:Y.45, C:W.48 Metal complexes: C:H.70 HEC.32: 23 residues within 4Å: Chain A: F.189 Chain I: F.44, Q.47, F.48, G.51, F.52, M.54, Y.58, R.83, H.86, R.87, A.90, M.93, T.128, F.131, G.132, G.135, L.138, P.139, H.187, T.188, P.192 Chain J: E.78 19 PLIP interactions: 19 interactions with chain I, Hydrophobic interactions: I:F.44, I:Q.47, I:F.48, I:M.54, I:Y.58, I:R.87, I:T.128, I:F.131, I:F.131, I:F.131, I:F.131, I:L.138, I:P.192 Water bridges: I:R.83 Salt bridges: I:R.83, I:R.83, I:R.87 Metal complexes: I:H.86, I:H.187 HEC.33: 28 residues within 4Å: Chain I: Y.34, G.37, G.38, T.40, L.41, M.93, M.97, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, V.122, L.124, A.125, T.128, M.199, H.202, F.203, I.206, G.210, I.211, S.212 Ligands: HEC.34 23 PLIP interactions: 23 interactions with chain I, Hydrophobic interactions: I:T.40, I:V.101, I:V.104, I:T.117, I:W.118, I:W.118, I:V.122, I:L.124, I:L.124, I:A.125, I:F.203, I:I.211 Hydrogen bonds: I:G.37, I:G.38, I:S.212 Water bridges: I:R.114 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 pi-Cation interactions: I:H.100 Metal complexes: I:H.100, I:H.202 HEC.34: 20 residues within 4Å: Chain I: V.30, N.31, Y.34, C.35, G.38, L.41, F.203, I.206, R.207, G.210, I.211 Chain J: N.25, F.40, V.43, I.44 Chain P: R.26 Ligands: HEC.33, 2WM.40, 8K6.42, UMQ.43 16 PLIP interactions: 5 interactions with chain J, 10 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:V.43, J:V.43, J:I.44, I:V.30, I:V.30, I:F.203, I:F.203, I:F.203, I:I.211 Hydrogen bonds: J:N.25, I:I.211 pi-Stacking: J:F.40 Water bridges: I:R.207, I:R.207 Salt bridges: I:R.207 Metal complexes: H2O.4 HEC.47: 20 residues within 4Å: Chain K: Y.45, P.46, W.48, A.49, C.66, C.69, H.70, Q.104, L.114, N.115, V.116, G.117, A.118, V.119, N.198, G.200, R.201, G.202, V.204, Y.205 20 PLIP interactions: 20 interactions with chain K, Hydrophobic interactions: K:Y.45, K:P.46, K:W.48, K:W.48, K:N.115, K:V.119, K:R.201, K:Y.205, K:Y.205 Hydrogen bonds: K:Q.104, K:N.115, K:N.115, K:N.115, K:G.200, K:Y.205 Water bridges: K:Y.45 Salt bridges: K:R.201 pi-Stacking: K:Y.45, K:W.48 Metal complexes: K:H.70

10 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.4: 4 residues within 4Å: Chain A: Y.5, A.18 Ligands: UMQ.10, SQD.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.5 UMQ.10: 10 residues within 4Å: Chain A: Q.15, A.18, E.19, V.21, T.22 Chain B: W.32 Chain C: N.332 Ligands: UMQ.4, UMQ.12, SQD.22 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:A.18, A:V.21, B:W.32, B:W.32 Hydrogen bonds: A:Q.15, A:E.19, C:N.332 UMQ.12: 11 residues within 4Å: Chain A: K.24, R.207 Chain B: A.31, L.36, F.40, P.41, M.45 Chain D: V.30 Ligands: HEC.3, UMQ.10, 8K6.11 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:V.30, B:P.41, B:P.41 Hydrogen bonds: A:R.207 Water bridges: A:R.207 UMQ.19: 6 residues within 4Å: Chain C: L.311 Chain D: G.14, F.18, L.22 Chain E: L.25, I.30 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: C:L.311, D:L.22, E:L.25 Hydrogen bonds: D:G.14 UMQ.30: 7 residues within 4Å: Chain B: F.124 Chain G: A.19, Y.26, Y.29, K.30 Ligands: 7PH.15, BCR.31 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: G:Y.26, G:Y.26, B:F.124 Hydrogen bonds: G:Y.26, G:Y.29, G:K.30 UMQ.35: 4 residues within 4Å: Chain I: Y.5, A.18 Ligands: UMQ.41, SQD.53 No protein-ligand interaction detected (PLIP) UMQ.41: 10 residues within 4Å: Chain I: Q.15, A.18, E.19, V.21, T.22 Chain J: W.32 Chain K: N.332 Ligands: UMQ.35, UMQ.43, SQD.53 8 PLIP interactions: 5 interactions with chain I, 2 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: I:A.18, I:V.21, J:W.32, J:W.32 Hydrogen bonds: I:Q.15, I:E.19, I:E.19, K:N.332 UMQ.43: 11 residues within 4Å: Chain I: K.24, R.207 Chain J: A.31, L.36, F.40, P.41, M.45 Chain L: V.30 Ligands: HEC.34, UMQ.41, 8K6.42 5 PLIP interactions: 1 interactions with chain L, 2 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: L:V.30, J:P.41, J:P.41 Hydrogen bonds: I:R.207 Water bridges: I:R.207 UMQ.50: 6 residues within 4Å: Chain K: L.311 Chain L: G.14, F.18, L.22 Chain M: L.25, I.30 4 PLIP interactions: 1 interactions with chain M, 2 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: M:L.25, L:L.22, K:L.311 Hydrogen bonds: L:G.14 UMQ.61: 7 residues within 4Å: Chain J: F.124 Chain O: A.19, Y.26, Y.29, K.30 Ligands: 7PH.46, BCR.62 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain J Hydrophobic interactions: O:Y.26, O:Y.26, J:F.124 Hydrogen bonds: O:K.30

10 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)

7PH.5: 4 residues within 4Å: Chain A: V.4, W.7 Chain J: F.113 Ligands: 8K6.38 6 PLIP interactions: 2 interactions with chain J, 4 interactions with chain A Hydrophobic interactions: J:F.113, J:F.113, A:V.4, A:W.7, A:W.7, A:W.7 7PH.15: 9 residues within 4Å: Chain B: F.124, P.127, T.130, T.131, L.134 Chain G: L.18, A.19, F.22 Ligands: UMQ.30 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain G Hydrophobic interactions: B:T.131, G:L.18, G:F.22, G:F.22 7PH.18: 8 residues within 4Å: Chain C: A.296, N.297, G.300, W.301, I.303, A.304 Chain E: F.10 Chain H: I.3 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:W.301, C:W.301, C:I.303, E:F.10 7PH.21: 10 residues within 4Å: Chain A: F.78 Chain B: V.52, V.56 Chain C: D.295, N.297, R.298, W.301, F.305 Chain D: G.33, Y.36 10 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C, 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: B:V.52, B:V.56, C:N.297, C:W.301, C:W.301, C:W.301, A:F.78, D:Y.36, D:Y.36 Hydrogen bonds: C:D.295 7PH.29: 7 residues within 4Å: Chain F: F.17, W.20, A.21, A.24 Chain G: Y.23 Ligands: 2WA.26, BCR.31 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.17, F:F.17, F:F.17, F:W.20, F:W.20, F:W.20, F:A.24 Salt bridges: F:K.28 7PH.36: 4 residues within 4Å: Chain B: F.113 Chain I: V.4, W.7 Ligands: 8K6.7 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain B Hydrophobic interactions: I:V.4, I:W.7, I:W.7, I:W.7, B:F.113, B:F.113 7PH.46: 9 residues within 4Å: Chain J: F.124, P.127, T.130, T.131, L.134 Chain O: L.18, A.19, F.22 Ligands: UMQ.61 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain J Hydrophobic interactions: O:L.18, O:F.22, O:F.22, J:T.131 7PH.49: 8 residues within 4Å: Chain K: A.296, N.297, G.300, W.301, I.303, A.304 Chain M: F.10 Chain P: I.3 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain M Hydrophobic interactions: K:W.301, K:W.301, K:I.303, M:F.10 7PH.52: 10 residues within 4Å: Chain I: F.78 Chain J: V.52, V.56 Chain K: D.295, N.297, R.298, W.301, F.305 Chain L: G.33, Y.36 9 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I, 4 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: J:V.52, J:V.56, I:F.78, K:N.297, K:W.301, K:W.301, K:W.301, L:Y.36, L:Y.36 7PH.60: 7 residues within 4Å: Chain N: F.17, W.20, A.21, A.24 Chain O: Y.23 Ligands: 2WA.57, BCR.62 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:F.17, N:F.17, N:F.17, N:W.20, N:W.20, N:W.20, N:A.24 Salt bridges: N:K.28

8 x 8K6: Octadecane(Non-covalent)

8K6.6: 7 residues within 4Å: Chain A: V.197, F.198, L.200, F.201 Ligands: 8K6.7, 8K6.8, CLA.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.198, A:F.198, A:L.200 8K6.7: 7 residues within 4Å: Chain A: V.119, F.201, M.205, K.208 Chain I: L.12 Ligands: 8K6.6, 7PH.36 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:V.119, A:F.201, A:K.208, I:L.12 8K6.8: 5 residues within 4Å: Chain A: S.130, T.134, L.169, A.186 Ligands: 8K6.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.134, A:L.169 8K6.11: 6 residues within 4Å: Chain B: L.36, F.40, P.41, M.45 Ligands: HEC.3, UMQ.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.40, B:P.41 8K6.37: 7 residues within 4Å: Chain I: V.197, F.198, L.200, F.201 Ligands: 8K6.38, 8K6.39, CLA.44 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:F.198, I:F.198, I:L.200 8K6.38: 7 residues within 4Å: Chain A: L.12 Chain I: V.119, F.201, M.205, K.208 Ligands: 7PH.5, 8K6.37 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain I Hydrophobic interactions: A:L.12, I:V.119, I:F.201, I:K.208 8K6.39: 5 residues within 4Å: Chain I: S.130, T.134, L.169, A.186 Ligands: 8K6.37 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:T.134, I:L.169 8K6.42: 6 residues within 4Å: Chain J: L.36, F.40, P.41, M.45 Ligands: HEC.34, UMQ.43 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:F.40, J:P.41

2 x 2WM: (1S,8E)-1-{[(2S)-3-hydroxy-2-{[(1S)-1-hydroxyoctadecyl]oxy}propyl]oxy}octadec-8-en-1-ol(Non-covalent)

2WM.9: 12 residues within 4Å: Chain A: L.41, L.45, F.48, F.52, F.203 Chain B: I.44, F.48 Chain D: A.34, V.38 Chain I: L.194, V.197 Ligands: HEC.3 11 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D, 4 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: A:L.45, A:F.48, A:F.48, A:F.52, D:V.38, B:I.44, B:I.44, B:F.48, B:F.48, I:L.194, I:V.197 2WM.40: 12 residues within 4Å: Chain A: L.194, V.197 Chain I: L.41, L.45, F.48, F.52, F.203 Chain J: I.44, F.48 Chain L: A.34, V.38 Ligands: HEC.34 11 PLIP interactions: 4 interactions with chain I, 1 interactions with chain L, 4 interactions with chain J, 2 interactions with chain A Hydrophobic interactions: I:L.45, I:F.48, I:F.48, I:F.52, L:V.38, J:I.44, J:I.44, J:F.48, J:F.48, A:L.194, A:V.197

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.13: 23 residues within 4Å: Chain A: I.98, F.102, Y.105, W.118, A.125, V.129 Chain B: Y.80, L.81, P.83, V.84, M.101, A.102, V.104, L.108, I.109, V.132, F.133, G.136, V.139, T.140 Ligands: 8K6.6, OPC.14, 2WA.26 18 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.81, B:V.84, B:A.102, B:V.104, B:L.108, B:I.109, B:V.132, B:F.133, B:V.139, A:I.98, A:F.102, A:Y.105, A:Y.105, A:W.118, A:V.129 Water bridges: B:V.84 pi-Stacking: B:F.133 Metal complexes: H2O.2 CLA.44: 23 residues within 4Å: Chain I: I.98, F.102, Y.105, W.118, A.125, V.129 Chain J: Y.80, L.81, P.83, V.84, M.101, A.102, V.104, L.108, I.109, V.132, F.133, G.136, V.139, T.140 Ligands: 8K6.37, OPC.45, 2WA.57 18 PLIP interactions: 11 interactions with chain J, 6 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:L.81, J:V.84, J:A.102, J:V.104, J:L.108, J:I.109, J:V.132, J:F.133, J:V.139, I:I.98, I:F.102, I:Y.105, I:Y.105, I:W.118, I:V.129 Water bridges: J:V.84 pi-Stacking: J:F.133 Metal complexes: H2O.5

2 x OPC: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE(Non-covalent)

OPC.14: 15 residues within 4Å: Chain A: Y.105 Chain B: I.87, A.100, S.103, G.107, L.108, V.111, I.114, E.115, N.118, R.126, P.127, V.128, A.129 Ligands: CLA.13 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.87, B:L.108, B:V.111, B:I.114 Hydrogen bonds: B:N.118, B:R.126, B:V.128, B:A.129 Water bridges: A:K.111 OPC.45: 15 residues within 4Å: Chain I: Y.105 Chain J: I.87, A.100, S.103, G.107, L.108, V.111, I.114, E.115, N.118, R.126, P.127, V.128, A.129 Ligands: CLA.44 11 PLIP interactions: 9 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:I.87, J:L.108, J:V.111, J:I.114 Hydrogen bonds: J:E.115, J:N.118, J:R.126, J:V.128, J:A.129, I:Y.105 Water bridges: I:K.111

2 x CD: CADMIUM ION(Non-covalent)

CD.17: 3 residues within 4Å: Chain A: E.75 Chain C: K.184, H.187 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Metal complexes: A:E.75, C:H.187 CD.48: 3 residues within 4Å: Chain I: E.75 Chain K: K.184, H.187 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain K Metal complexes: I:E.75, K:H.187

2 x MYS: PENTADECANE(Non-covalent)

MYS.20: 3 residues within 4Å: Chain D: F.42 Chain I: L.168 Ligands: 2WD.24 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain I Hydrophobic interactions: D:F.42, I:L.168 MYS.51: 3 residues within 4Å: Chain A: L.168 Chain L: F.42 Ligands: 2WD.55 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain A Hydrophobic interactions: L:F.42, A:L.168

2 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.22: 13 residues within 4Å: Chain B: W.32, P.33, Y.38 Chain C: K.319 Chain D: R.16, N.20, F.24, G.25, T.28, G.29, A.31 Ligands: UMQ.4, UMQ.10 9 PLIP interactions: 1 interactions with chain B, 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:W.32, D:R.16, D:N.20, D:N.20 Hydrophobic interactions: D:N.20, D:F.24, D:F.24, D:A.31 Salt bridges: C:K.319 SQD.53: 13 residues within 4Å: Chain J: W.32, P.33, Y.38 Chain K: K.319 Chain L: R.16, N.20, F.24, G.25, T.28, G.29, A.31 Ligands: UMQ.35, UMQ.41 9 PLIP interactions: 1 interactions with chain J, 7 interactions with chain L, 1 interactions with chain K Hydrogen bonds: J:W.32, L:R.16, L:N.20, L:N.20 Hydrophobic interactions: L:N.20, L:F.24, L:F.24, L:A.31 Salt bridges: K:K.319

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.23: 10 residues within 4Å: Chain D: C.108, H.110, L.111, G.112, C.113, C.126, C.128, H.129, G.130, S.131 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.108, D:H.110, D:C.126, D:H.129 FES.54: 10 residues within 4Å: Chain L: C.108, H.110, L.111, G.112, C.113, C.126, C.128, H.129, G.130, S.131 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.108, L:H.110, L:C.126, L:H.129

2 x 2WD: (1R)-1-{[(2S)-3-hydroxy-2-{[(1R)-1-hydroxypentyl]oxy}propyl]oxy}hexan-1-ol(Non-covalent)

2WD.24: 7 residues within 4Å: Chain D: L.35, Y.36, V.39, N.40, I.43 Chain I: L.164 Ligands: MYS.20 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.35, D:Y.36 2WD.55: 7 residues within 4Å: Chain A: L.164 Chain L: L.35, Y.36, V.39, N.40, I.43 Ligands: MYS.51 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:L.35, L:Y.36

2 x 3WM: (1S,8E,1'R,8'Z)-1,1'-{[(2S)-3-hydroxypropane-1,2-diyl]bis(oxy)}bisoctadec-8-en-1-ol(Non-covalent)

3WM.25: 23 residues within 4Å: Chain A: I.39, C.43, M.92, M.96 Chain B: C.50 Chain C: Q.82, S.83 Chain E: A.3, I.4, Y.7, I.8 Chain F: E.4, A.8, L.11, S.12, V.18 Chain G: L.5 Chain H: T.5, W.8, L.12, F.15 Ligands: 1O2.28, BCR.31 16 PLIP interactions: 2 interactions with chain A, 4 interactions with chain H, 4 interactions with chain F, 5 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: A:I.39, A:M.92, H:W.8, H:F.15, H:F.15, F:L.11, F:L.11, F:V.18, E:A.3, E:I.4, E:Y.7, E:Y.7, E:I.8 Hydrogen bonds: H:T.5, F:E.4, C:S.83 3WM.56: 23 residues within 4Å: Chain I: I.39, C.43, M.92, M.96 Chain J: C.50 Chain K: Q.82, S.83 Chain M: A.3, I.4, Y.7, I.8 Chain N: E.4, A.8, L.11, S.12, V.18 Chain O: L.5 Chain P: T.5, W.8, L.12, F.15 Ligands: 1O2.59, BCR.62 15 PLIP interactions: 2 interactions with chain I, 5 interactions with chain M, 3 interactions with chain N, 1 interactions with chain K, 4 interactions with chain P Hydrophobic interactions: I:I.39, I:M.92, M:A.3, M:I.4, M:Y.7, M:Y.7, M:I.8, N:L.11, N:L.11, N:V.18, P:W.8, P:F.15, P:F.15 Hydrogen bonds: K:S.83, P:T.5

2 x 2WA: (1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol(Non-covalent)

2WA.26: 17 residues within 4Å: Chain A: F.102 Chain B: W.79, T.140, L.141, G.144, I.145, A.148 Chain F: M.1, S.2, L.5, A.9, F.13 Chain G: V.2, L.11, I.14 Ligands: CLA.13, 7PH.29 9 PLIP interactions: 2 interactions with chain G, 2 interactions with chain B, 4 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: G:V.2, G:I.14, B:T.140, B:L.141, F:L.5, F:L.5, F:A.9, F:F.13, A:F.102 2WA.57: 17 residues within 4Å: Chain I: F.102 Chain J: W.79, T.140, L.141, G.144, I.145, A.148 Chain N: M.1, S.2, L.5, A.9, F.13 Chain O: V.2, L.11, I.14 Ligands: CLA.44, 7PH.60 9 PLIP interactions: 4 interactions with chain N, 2 interactions with chain O, 2 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: N:L.5, N:L.5, N:A.9, N:F.13, O:V.2, O:I.14, J:T.140, J:L.141, I:F.102

2 x OCT: N-OCTANE(Non-covalent)

OCT.27: 4 residues within 4Å: Chain F: N.7, L.10, L.11, G.14 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.11 OCT.58: 4 residues within 4Å: Chain N: N.7, L.10, L.11, G.14 1 PLIP interactions: 1 interactions with chain N Hydrophobic interactions: N:L.11

2 x 1O2: (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate(Non-covalent)

1O2.28: 10 residues within 4Å: Chain E: I.8, L.11, A.12, T.15, G.16, F.23 Chain F: K.28, I.29, G.31 Ligands: 3WM.25 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:L.11, E:A.12, E:T.15, E:F.23, E:F.23, F:I.29 Hydrogen bonds: F:G.31 1O2.59: 10 residues within 4Å: Chain M: I.8, L.11, A.12, T.15, G.16, F.23 Chain N: K.28, I.29, G.31 Ligands: 3WM.56 7 PLIP interactions: 2 interactions with chain N, 5 interactions with chain M Hydrophobic interactions: N:I.29, M:L.11, M:A.12, M:T.15, M:F.23, M:F.23 Hydrogen bonds: N:G.31

2 x BCR: BETA-CAROTENE(Non-covalent)

BCR.31: 21 residues within 4Å: Chain A: I.32, F.33, I.39, M.96, L.99 Chain F: I.16, F.17, W.20 Chain G: V.16, T.17, A.19, G.20, Y.23, Y.26 Chain H: F.15, S.18, I.19, V.22 Ligands: 3WM.25, 7PH.29, UMQ.30 19 PLIP interactions: 7 interactions with chain G, 5 interactions with chain A, 5 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: G:V.16, G:A.19, G:Y.23, G:Y.23, G:Y.23, G:Y.23, G:Y.26, A:I.32, A:F.33, A:F.33, A:I.39, A:L.99, F:I.16, F:I.16, F:F.17, F:F.17, F:W.20, H:F.15, H:V.22 BCR.62: 21 residues within 4Å: Chain I: I.32, F.33, I.39, M.96, L.99 Chain N: I.16, F.17, W.20 Chain O: V.16, T.17, A.19, G.20, Y.23, Y.26 Chain P: F.15, S.18, I.19, V.22 Ligands: 3WM.56, 7PH.60, UMQ.61 19 PLIP interactions: 5 interactions with chain N, 7 interactions with chain O, 2 interactions with chain P, 5 interactions with chain I Hydrophobic interactions: N:I.16, N:I.16, N:F.17, N:F.17, N:W.20, O:V.16, O:A.19, O:Y.23, O:Y.23, O:Y.23, O:Y.23, O:Y.26, P:F.15, P:V.22, I:I.32, I:F.33, I:F.33, I:I.39, I:L.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasan, S.S. et al., Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome b6f Complex. Structure (2014)

Release Date

2014-05-14

Peptides

Cytochrome b6: AI
Cytochrome b6-f complex subunit 4: BJ
Apocytochrome f: CK
Cytochrome b6-f complex iron-sulfur subunit 1: DL
Cytochrome b6-f complex subunit 6: EM
Cytochrome b6-f complex subunit 7: FN
Cytochrome b6-f complex subunit 5: GO
Cytochrome b6-f complex subunit 8: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

I
A

B
B

J
B

C
C

K
C

D
D

L
D

E
E

M
E

F
F

N
F

G
G

O
G

H
H

P
H

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b6

Cytochrome b6-f complex subunit 4

Apocytochrome f

Cytochrome b6-f complex iron-sulfur subunit 1

Cytochrome b6-f complex subunit 6

Cytochrome b6-f complex subunit 7

Cytochrome b6-f complex subunit 5

Cytochrome b6-f complex subunit 8

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