SMTL ID : 2e74.1

Crystal Structure of the Cytochrome b6f Complex from M.laminosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-oligomer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: E.75 Chain C: K.140, H.143 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:E.75, C:H.143, H2O.1, H2O.5 CD.9: 4 residues within 4Å: Chain B: D.58 Chain C: K.146 Chain F: E.4 Chain G: E.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.58 CD.17: 3 residues within 4Å: Chain I: E.75 Chain K: K.140, H.143 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: I:E.75, K:H.143, H2O.6, H2O.10 CD.25: 4 residues within 4Å: Chain J: D.58 Chain K: K.146 Chain N: E.4 Chain O: E.3 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.58

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

HEM.2: 23 residues within 4Å: Chain A: F.44, Q.47, G.51, F.52, M.54, T.55, Y.58, R.83, H.86, R.87, A.90, M.93, F.131, G.132, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192 Chain I: F.189 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain I, Hydrophobic interactions: A:F.44, A:Q.47, A:Q.47, A:F.52, A:M.54, A:T.55, A:Y.58, A:A.90, A:F.131, A:F.131, A:L.138, A:Y.184, A:P.192, I:F.189 Salt bridges: A:R.83, A:R.83, A:R.87 Metal complexes: A:H.86, A:H.187 HEM.3: 27 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, I.211, S.212 Ligands: HEM.4 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:T.40, A:V.101, A:V.104, A:V.104, A:T.117, A:W.118, A:W.118, A:W.118, A:V.122, A:L.124, A:L.124, A:A.125, A:I.206 Hydrogen bonds: A:G.37, A:G.38, A:S.212 Water bridges: A:Y.34 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 Metal complexes: A:H.100, A:H.202 HEM.4: 19 residues within 4Å: Chain A: V.30, N.31, Y.34, C.35, G.38, L.41, T.42, F.203, I.206, R.207, G.210, I.211 Chain B: N.25, V.39, F.40, V.43, I.44 Chain H: R.26 Ligands: HEM.3 15 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.30, A:Y.34, A:F.203, A:I.206, A:I.211, B:V.39, B:F.40, B:F.40, B:F.40, B:V.43, B:I.44, B:I.44 Hydrogen bonds: A:I.211 Salt bridges: A:R.207 Metal complexes: H2O.2 HEM.12: 20 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.1, C:P.2, C:W.4, C:W.4, C:W.4, C:A.5, C:N.154, C:R.157, C:Y.161, C:Y.161, C:P.162 Hydrogen bonds: C:N.71, C:N.71, C:N.71 Salt bridges: C:R.157 pi-Stacking: C:Y.1, C:W.4 Metal complexes: C:H.26 HEM.18: 23 residues within 4Å: Chain A: F.189 Chain I: F.44, Q.47, G.51, F.52, M.54, T.55, Y.58, R.83, H.86, R.87, A.90, M.93, F.131, G.132, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192 19 PLIP interactions: 18 interactions with chain I, 1 interactions with chain A, Hydrophobic interactions: I:F.44, I:Q.47, I:Q.47, I:F.52, I:M.54, I:T.55, I:Y.58, I:A.90, I:F.131, I:F.131, I:L.138, I:Y.184, I:P.192, A:F.189 Salt bridges: I:R.83, I:R.83, I:R.87 Metal complexes: I:H.86, I:H.187 HEM.19: 27 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, I.211, S.212 Ligands: HEM.20 23 PLIP interactions: 23 interactions with chain I, Hydrophobic interactions: I:T.40, I:V.101, I:V.104, I:V.104, I:T.117, I:W.118, I:W.118, I:W.118, I:V.122, I:L.124, I:L.124, I:A.125, I:I.206 Hydrogen bonds: I:G.37, I:G.38, I:S.212 Water bridges: I:Y.34 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 Metal complexes: I:H.100, I:H.202 HEM.20: 19 residues within 4Å: Chain I: V.30, N.31, Y.34, C.35, G.38, L.41, T.42, F.203, I.206, R.207, G.210, I.211 Chain J: N.25, V.39, F.40, V.43, I.44 Chain P: R.26 Ligands: HEM.19 15 PLIP interactions: 7 interactions with chain J, 7 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:V.39, J:F.40, J:F.40, J:F.40, J:V.43, J:I.44, J:I.44, I:V.30, I:Y.34, I:F.203, I:I.206, I:I.211 Hydrogen bonds: I:I.211 Salt bridges: I:R.207 Metal complexes: H2O.7 HEM.28: 20 residues within 4Å: Chain K: Y.1, P.2, W.4, A.5, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 19 PLIP interactions: 19 interactions with chain K, Hydrophobic interactions: K:Y.1, K:P.2, K:W.4, K:W.4, K:W.4, K:A.5, K:N.154, K:R.157, K:Y.161, K:Y.161, K:P.162 Hydrogen bonds: K:N.71, K:N.71, K:N.71, K:Y.161 Salt bridges: K:R.157 pi-Stacking: K:Y.1, K:W.4 Metal complexes: K:H.26

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

UMQ.5: 13 residues within 4Å: Chain A: N.74, E.75, F.78, W.80, L.81 Chain B: V.52 Chain C: N.253, R.254, W.257, M.258, F.261 Chain D: A.34, P.37 14 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: C:R.254, C:W.257, C:F.261, C:F.261, C:F.261, B:V.52, D:P.37, A:F.78, A:W.80, A:L.81 Hydrogen bonds: C:N.253, A:E.75, A:F.78, A:W.80 UMQ.6: 8 residues within 4Å: Chain A: L.116, L.201, K.208 Chain I: L.12, E.13, A.16 Ligands: UMQ.22, UMQ.23 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:L.116, A:L.201 Hydrogen bonds: A:K.208, I:E.13 Salt bridges: A:K.208 UMQ.7: 7 residues within 4Å: Chain A: N.3, Y.5, D.6, I.14, Q.15 Ligands: UMQ.8, UMQ.22 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.5, A:I.14 Hydrogen bonds: A:N.3, A:D.6, A:Q.15, A:Q.15 UMQ.8: 6 residues within 4Å: Chain A: A.18, D.19, T.22 Chain B: W.32 Ligands: UMQ.7, SQD.14 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.32, B:W.32, A:A.18 Hydrogen bonds: A:Q.15, A:T.22 UMQ.21: 13 residues within 4Å: Chain I: N.74, E.75, F.78, W.80, L.81 Chain J: V.52 Chain K: N.253, R.254, W.257, M.258, F.261 Chain L: A.34, P.37 14 PLIP interactions: 6 interactions with chain I, 6 interactions with chain K, 1 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: I:F.78, I:W.80, I:L.81, K:R.254, K:W.257, K:F.261, K:F.261, K:F.261, L:P.37, J:V.52 Hydrogen bonds: I:E.75, I:F.78, I:W.80, K:N.253 UMQ.22: 8 residues within 4Å: Chain A: L.12, E.13, A.16 Chain I: L.116, L.201, K.208 Ligands: UMQ.6, UMQ.7 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain A Hydrophobic interactions: I:L.116, I:L.201 Hydrogen bonds: I:K.208, A:E.13 Salt bridges: I:K.208 UMQ.23: 7 residues within 4Å: Chain I: N.3, Y.5, D.6, I.14, Q.15 Ligands: UMQ.6, UMQ.24 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:Y.5, I:I.14 Hydrogen bonds: I:N.3, I:D.6, I:Q.15, I:Q.15 UMQ.24: 6 residues within 4Å: Chain I: A.18, D.19, T.22 Chain J: W.32 Ligands: UMQ.23, SQD.30 7 PLIP interactions: 5 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: I:A.18, J:W.32, J:W.32 Hydrogen bonds: I:Q.15, I:D.19, I:T.22, I:T.22

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.10: 21 residues within 4Å: Chain A: I.98, V.101, F.102, Y.105, A.125, V.129 Chain B: Y.80, P.83, V.84, I.87, M.101, V.104, P.105, L.106, L.108, I.132, F.133, G.136, V.139, T.140 Ligands: OPC.11 15 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.101, A:F.102, A:Y.105, A:Y.105, A:V.129, B:V.84, B:I.87, B:V.104, B:V.104, B:P.105, B:L.106, B:I.132, B:F.133, B:V.139 Metal complexes: H2O.3 CLA.26: 21 residues within 4Å: Chain I: I.98, V.101, F.102, Y.105, A.125, V.129 Chain J: Y.80, P.83, V.84, I.87, M.101, V.104, P.105, L.106, L.108, I.132, F.133, G.136, V.139, T.140 Ligands: OPC.27 15 PLIP interactions: 5 interactions with chain I, 9 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: I:V.101, I:F.102, I:Y.105, I:Y.105, I:V.129, J:V.84, J:I.87, J:V.104, J:V.104, J:P.105, J:L.106, J:I.132, J:F.133, J:V.139 Metal complexes: H2O.8

4 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.11: 17 residues within 4Å: Chain A: Y.105 Chain B: I.87, L.100, S.103, V.104, L.108, V.111, I.114, E.115, V.117, N.118, R.126, P.127, V.128, A.129, I.132 Ligands: CLA.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.87, B:L.100, B:L.108, B:I.132 Hydrogen bonds: B:E.115, B:N.118, B:R.126, B:V.128, B:A.129 OPC.16: 19 residues within 4Å: Chain A: M.92, M.96 Chain B: C.50 Chain C: Q.38 Chain E: G.4, A.5, Y.8 Chain F: Y.7, A.8, L.11, S.12, G.14 Chain G: L.5, L.9 Chain H: W.8, L.11, L.12, F.15 Ligands: BCR.15 14 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 7 interactions with chain H, 1 interactions with chain E, 2 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: A:M.92, H:W.8, H:L.11, H:L.11, H:L.12, H:F.15, H:F.15, H:F.15, E:Y.8, F:A.8, F:L.11, G:L.5, G:L.9 Hydrogen bonds: C:Q.38 OPC.27: 17 residues within 4Å: Chain I: Y.105 Chain J: I.87, L.100, S.103, V.104, L.108, V.111, I.114, E.115, V.117, N.118, R.126, P.127, V.128, A.129, I.132 Ligands: CLA.26 9 PLIP interactions: 1 interactions with chain I, 8 interactions with chain J Hydrogen bonds: I:Y.105, J:N.118, J:R.126, J:V.128, J:A.129 Hydrophobic interactions: J:I.87, J:L.100, J:L.108, J:I.132 OPC.32: 19 residues within 4Å: Chain I: M.92, M.96 Chain J: C.50 Chain K: Q.38 Chain M: G.4, A.5, Y.8 Chain N: Y.7, A.8, L.11, S.12, G.14 Chain O: L.5, L.9 Chain P: W.8, L.11, L.12, F.15 Ligands: BCR.31 14 PLIP interactions: 2 interactions with chain N, 1 interactions with chain K, 1 interactions with chain M, 1 interactions with chain I, 7 interactions with chain P, 2 interactions with chain O Hydrophobic interactions: N:A.8, N:L.11, M:Y.8, I:M.92, P:W.8, P:L.11, P:L.11, P:L.12, P:F.15, P:F.15, P:F.15, O:L.5, O:L.9 Hydrogen bonds: K:Q.38

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.13: 10 residues within 4Å: Chain D: C.108, H.110, L.111, C.113, C.126, C.128, H.129, G.130, S.131, P.143 5 PLIP interactions: 5 interactions with chain D, Metal complexes: D:C.108, D:H.110, D:C.126, D:H.129, D:S.131 FES.29: 10 residues within 4Å: Chain L: C.108, H.110, L.111, C.113, C.126, C.128, H.129, G.130, S.131, P.143 5 PLIP interactions: 5 interactions with chain L, Metal complexes: L:C.108, L:H.110, L:C.126, L:H.129, L:S.131

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

SQD.14: 8 residues within 4Å: Chain B: W.32, Y.38 Chain C: K.275 Chain D: R.16, N.20, L.21, G.25 Ligands: UMQ.8 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.21 Hydrogen bonds: D:R.16, D:N.20, D:N.20 Salt bridges: C:K.275 SQD.30: 8 residues within 4Å: Chain J: W.32, Y.38 Chain K: K.275 Chain L: R.16, N.20, L.21, G.25 Ligands: UMQ.24 6 PLIP interactions: 1 interactions with chain K, 4 interactions with chain L, 1 interactions with chain J Salt bridges: K:K.275 Hydrophobic interactions: L:L.21 Hydrogen bonds: L:R.16, L:N.20, L:N.20, J:Y.38

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

BCR.15: 19 residues within 4Å: Chain A: I.32, F.33, I.39, M.96, L.99 Chain B: T.47 Chain F: I.16, F.17, W.20 Chain G: L.13, A.16, T.17, G.19, G.20, Y.23 Chain H: F.15, S.18, I.19 Ligands: OPC.16 16 PLIP interactions: 6 interactions with chain A, 4 interactions with chain F, 4 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: A:I.32, A:I.32, A:I.32, A:F.33, A:F.33, A:L.99, F:I.16, F:I.16, F:F.17, F:W.20, G:L.13, G:Y.23, G:Y.23, G:Y.23, H:F.15, H:I.19 BCR.31: 19 residues within 4Å: Chain I: I.32, F.33, I.39, M.96, L.99 Chain J: T.47 Chain N: I.16, F.17, W.20 Chain O: L.13, A.16, T.17, G.19, G.20, Y.23 Chain P: F.15, S.18, I.19 Ligands: OPC.32 16 PLIP interactions: 4 interactions with chain O, 6 interactions with chain I, 2 interactions with chain P, 4 interactions with chain N Hydrophobic interactions: O:L.13, O:Y.23, O:Y.23, O:Y.23, I:I.32, I:I.32, I:I.32, I:F.33, I:F.33, I:L.99, P:F.15, P:I.19, N:I.16, N:I.16, N:F.17, N:W.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamashita, E. et al., Structure of the Cytochrome b(6)f Complex: Quinone Analogue Inhibitors as Ligands of Heme c(n). J.Mol.Biol. (2007)

Release Date

2007-06-12

Peptides

Cytochrome b6: AI
Cytochrome b6-f complex subunit 4: BJ
Apocytochrome f: CK
Cytochrome b6-f complex iron-sulfur subunit: 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

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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