SMTL ID : 2e75.1

Crystal Structure of the Cytochrome b6f Complex with 2-nonyl-4-hydroxyquinoline N-oxide (NQNO) from M.laminosus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.55 Å

Oligo State

hetero-oligomer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: E.75 Chain C: H.143 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.143, A:E.75, A:E.75, H2O.1, H2O.2 CD.10: 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.18: 2 residues within 4Å: Chain I: E.75 Chain K: H.143 5 PLIP interactions: 1 interactions with chain K, 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: K:H.143, I:E.75, I:E.75, H2O.6, H2O.7 CD.27: 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(Covalent)(Non-covalent)

HEM.2: 23 residues within 4Å: Chain A: Q.47, F.48, 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 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain I, Hydrophobic interactions: A:Q.47, A:Q.47, A:F.48, A:T.55, A:Y.58, A:A.90, A:F.131, A:F.131, A:L.138, A:Y.184, A:T.188, 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: 25 residues within 4Å: Chain A: Y.34, G.37, G.38, T.40, L.41, 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, H.202, F.203, I.206, I.211, S.212 Ligands: HEM.4 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:V.101, A:V.104, A:T.117, A:W.118, A:W.118, A:W.118, A:V.122, A:L.124, A:A.125, A:F.203, 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: 18 residues within 4Å: Chain A: V.30, 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 Ligands: HEM.3, QNO.9 16 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.30, A:L.41, A:F.203, A:F.203, A:I.206, A:R.207, A:I.211, B:V.39, B:F.40, B:F.40, B:F.40, B:V.43, B:I.44 Hydrogen bonds: A:I.211 Salt bridges: A:R.207 Metal complexes: H2O.3 HEM.13: 21 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, V.75, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:Y.1, C:P.2, C:A.5, C:V.75, C:Y.161, C:Y.161 Hydrogen bonds: C:Q.60, 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.19: 23 residues within 4Å: Chain A: F.189 Chain I: Q.47, F.48, 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 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain I, Hydrophobic interactions: A:F.189, I:Q.47, I:Q.47, I:F.48, I:T.55, I:Y.58, I:A.90, I:F.131, I:F.131, I:L.138, I:Y.184, I:T.188, I:P.192 Salt bridges: I:R.83, I:R.83, I:R.87 Metal complexes: I:H.86, I:H.187 HEM.20: 25 residues within 4Å: Chain I: Y.34, G.37, G.38, T.40, L.41, 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, H.202, F.203, I.206, I.211, S.212 Ligands: HEM.21 21 PLIP interactions: 21 interactions with chain I, Hydrophobic interactions: I:V.101, I:V.104, I:T.117, I:W.118, I:W.118, I:W.118, I:V.122, I:L.124, I:A.125, I:F.203, 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.21: 18 residues within 4Å: Chain I: V.30, 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 Ligands: HEM.20, QNO.26 16 PLIP interactions: 9 interactions with chain I, 6 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: I:V.30, I:L.41, I:F.203, I:F.203, I:I.206, I:R.207, I:I.211, J:V.39, J:F.40, J:F.40, J:F.40, J:V.43, J:I.44 Hydrogen bonds: I:I.211 Salt bridges: I:R.207 Metal complexes: H2O.8 HEM.30: 21 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, V.75, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 15 PLIP interactions: 15 interactions with chain K, Hydrophobic interactions: K:Y.1, K:P.2, K:A.5, K:V.75, K:Y.161, K:Y.161 Hydrogen bonds: K:Y.1, K:Q.60, 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

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.5: 17 residues within 4Å: Chain A: M.92 Chain B: C.50 Chain C: P.37, Q.38 Chain E: G.4, A.5, Y.8, I.9 Chain F: Y.7, A.8, S.12, V.18 Chain G: L.5, L.9 Chain H: V.5, W.8, F.15 12 PLIP interactions: 4 interactions with chain H, 2 interactions with chain F, 2 interactions with chain E, 2 interactions with chain G, 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: H:W.8, H:W.8, H:F.15, H:F.15, F:Y.7, F:V.18, E:Y.8, E:I.9, G:L.5, G:L.9, A:M.92 Hydrogen bonds: C:Q.38 OPC.12: 15 residues within 4Å: Chain A: Y.105 Chain B: I.87, L.100, S.103, L.108, V.111, I.114, E.115, N.118, R.125, R.126, P.127, V.128, A.129 Ligands: CLA.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.87, B:L.100, B:L.108, B:V.111, B:I.114 Hydrogen bonds: B:E.115, B:R.126, B:V.128, B:A.129 OPC.22: 17 residues within 4Å: Chain I: M.92 Chain J: C.50 Chain K: P.37, Q.38 Chain M: G.4, A.5, Y.8, I.9 Chain N: Y.7, A.8, S.12, V.18 Chain O: L.5, L.9 Chain P: V.5, W.8, F.15 12 PLIP interactions: 1 interactions with chain I, 2 interactions with chain O, 4 interactions with chain P, 2 interactions with chain N, 1 interactions with chain K, 2 interactions with chain M Hydrophobic interactions: I:M.92, O:L.5, O:L.9, P:W.8, P:W.8, P:F.15, P:F.15, N:Y.7, N:V.18, M:Y.8, M:I.9 Hydrogen bonds: K:Q.38 OPC.29: 15 residues within 4Å: Chain I: Y.105 Chain J: I.87, L.100, S.103, L.108, V.111, I.114, E.115, N.118, R.125, R.126, P.127, V.128, A.129 Ligands: CLA.28 10 PLIP interactions: 9 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:I.87, J:L.100, J:L.108, J:V.111, J:I.114 Hydrogen bonds: J:E.115, J:R.126, J:V.128, J:A.129, I:Y.105

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

UMQ.6: 8 residues within 4Å: Chain A: D.20, K.24, L.204, R.207, K.208 Chain I: L.12, L.17 Ligands: UMQ.24 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain A Hydrophobic interactions: I:L.12 Hydrogen bonds: A:K.24, A:K.24 Salt bridges: A:K.208 UMQ.7: 8 residues within 4Å: Chain A: N.3, Y.5, D.6, I.14, Q.15, A.18 Ligands: UMQ.8, UMQ.23 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.14 Hydrogen bonds: A:N.3, A:Q.15 UMQ.8: 7 residues within 4Å: Chain A: A.18, V.21, T.22 Chain B: W.32 Ligands: UMQ.7, QNO.9, SQD.16 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.18, A:V.21, A:T.22, B:W.32, B:W.32 Hydrogen bonds: A:T.22 UMQ.14: 13 residues within 4Å: Chain A: E.75, F.78, W.80, L.81 Chain B: V.52 Chain C: D.251, N.253, R.254, W.257, M.258, F.261 Chain D: A.34, P.37 15 PLIP interactions: 1 interactions with chain B, 8 interactions with chain C, 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:V.52, C:W.257, C:W.257, C:F.261, C:F.261, A:F.78, A:W.80, D:P.37 Hydrogen bonds: C:D.251, C:D.251, C:N.253, C:R.254, A:E.75, A:F.78, A:W.80 UMQ.23: 8 residues within 4Å: Chain A: L.12, L.17 Chain I: D.20, K.24, L.204, R.207, K.208 Ligands: UMQ.7 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain A Hydrogen bonds: I:K.24, I:K.24 Salt bridges: I:K.208 Hydrophobic interactions: A:L.12 UMQ.24: 8 residues within 4Å: Chain I: N.3, Y.5, D.6, I.14, Q.15, A.18 Ligands: UMQ.6, UMQ.25 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:I.14 Hydrogen bonds: I:N.3, I:Q.15 UMQ.25: 7 residues within 4Å: Chain I: A.18, V.21, T.22 Chain J: W.32 Ligands: UMQ.24, QNO.26, SQD.33 7 PLIP interactions: 2 interactions with chain J, 5 interactions with chain I Hydrophobic interactions: J:W.32, J:W.32, I:A.18, I:V.21, I:T.22 Hydrogen bonds: I:T.22, I:T.22 UMQ.31: 13 residues within 4Å: Chain I: E.75, F.78, W.80, L.81 Chain J: V.52 Chain K: D.251, N.253, R.254, W.257, M.258, F.261 Chain L: A.34, P.37 14 PLIP interactions: 7 interactions with chain K, 5 interactions with chain I, 1 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: K:W.257, K:W.257, K:F.261, K:F.261, I:F.78, I:W.80, J:V.52, L:P.37 Hydrogen bonds: K:D.251, K:N.253, K:R.254, I:E.75, I:F.78, I:W.80

2 x QNO: 2-NONYL-4-HYDROXYQUINOLINE N-OXIDE(Non-covalent)

QNO.9: 8 residues within 4Å: Chain A: K.24, R.207 Chain B: A.31, L.36, F.40, P.41 Ligands: HEM.4, UMQ.8 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.207, A:R.207 Hydrophobic interactions: B:A.31, B:F.40, B:P.41 QNO.26: 8 residues within 4Å: Chain I: K.24, R.207 Chain J: A.31, L.36, F.40, P.41 Ligands: HEM.21, UMQ.25 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:A.31, J:F.40, J:P.41 Hydrogen bonds: I:R.207, I:R.207

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.11: 20 residues within 4Å: Chain A: I.98, V.101, F.102, Y.105, I.123, V.129 Chain B: Y.80, P.83, V.84, I.87, M.101, V.104, P.105, L.108, I.132, F.133, G.136, V.139, T.140 Ligands: OPC.12 15 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.101, A:F.102, A:Y.105, A:Y.105, A:I.123, A:V.129, B:I.87, B:M.101, B:V.104, B:V.104, B:I.132, B:F.133, B:V.139 Hydrogen bonds: B:V.84 Metal complexes: H2O.4 CLA.28: 20 residues within 4Å: Chain I: I.98, V.101, F.102, Y.105, I.123, V.129 Chain J: Y.80, P.83, V.84, I.87, M.101, V.104, P.105, L.108, I.132, F.133, G.136, V.139, T.140 Ligands: OPC.29 15 PLIP interactions: 8 interactions with chain J, 6 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:I.87, J:M.101, J:V.104, J:V.104, J:I.132, J:F.133, J:V.139, I:V.101, I:F.102, I:Y.105, I:Y.105, I:I.123, I:V.129 Hydrogen bonds: J:V.84 Metal complexes: H2O.9

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

FES.15: 10 residues within 4Å: Chain D: C.108, H.110, L.111, G.112, C.113, C.126, 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.32: 10 residues within 4Å: Chain L: C.108, H.110, L.111, G.112, C.113, C.126, 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.16: 10 residues within 4Å: Chain B: W.32, P.33, Y.38 Chain C: K.275, V.279 Chain D: R.16, N.20, F.24, G.25 Ligands: UMQ.8 6 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:N.20, B:W.32, B:Y.38, B:Y.38 Salt bridges: D:R.16, C:K.275 SQD.33: 10 residues within 4Å: Chain J: W.32, P.33, Y.38 Chain K: K.275, V.279 Chain L: R.16, N.20, F.24, G.25 Ligands: UMQ.25 6 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K, 2 interactions with chain L Hydrogen bonds: J:W.32, J:Y.38, J:Y.38, L:N.20 Salt bridges: K:K.275, L:R.16

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

BCR.17: 15 residues within 4Å: Chain A: I.32, F.33, I.39, L.99 Chain B: V.43 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 16 PLIP interactions: 5 interactions with chain F, 4 interactions with chain A, 5 interactions with chain G, 1 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: F:I.16, F:I.16, F:F.17, F:F.17, F:W.20, A:I.32, A:F.33, A:I.39, A:L.99, G:L.13, G:A.16, G:Y.23, G:Y.23, G:Y.23, B:V.43, H:F.15 BCR.34: 15 residues within 4Å: Chain I: I.32, F.33, I.39, L.99 Chain J: V.43 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 16 PLIP interactions: 5 interactions with chain N, 4 interactions with chain I, 5 interactions with chain O, 1 interactions with chain P, 1 interactions with chain J Hydrophobic interactions: N:I.16, N:I.16, N:F.17, N:F.17, N:W.20, I:I.32, I:F.33, I:I.39, I:L.99, O:L.13, O:A.16, O:Y.23, O:Y.23, O:Y.23, P:F.15, J:V.43

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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