SMTL ID : 4h0l.1

Cytochrome b6f Complex Crystal Structure from Mastigocladus laminosus with n-Side Inhibitor NQNO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

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

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: E.75 Chain C: K.140, H.143 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:E.75, A:E.75, C:H.143 CD.10: 4 residues within 4Å: Chain B: D.58 Chain C: K.146 Chain F: E.4 Chain G: L.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.58 CD.18: 3 residues within 4Å: Chain I: E.75 Chain K: K.140, H.143 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain K Metal complexes: I:E.75, I:E.75, K:H.143 CD.27: 4 residues within 4Å: Chain J: D.58 Chain K: K.146 Chain N: E.4 Chain O: L.5 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.58

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

HEM.2: 29 residues within 4Å: Chain A: F.44, Q.47, F.48, G.51, F.52, M.54, T.55, Y.58, V.69, I.72, R.83, H.86, R.87, A.90, M.93, T.128, F.131, G.132, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192, I.195 Chain B: E.78 Chain I: F.189 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain I, Hydrophobic interactions: A:F.44, A:Q.47, A:M.54, A:Y.58, A:F.131, A:F.131, A:F.131, A:F.131, A:F.131, A:L.138, A:Y.184, I:F.189 Salt bridges: A:R.83, A:R.83, A:R.87 Metal complexes: A:H.86, A:H.187 HEM.3: 31 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, T.107, G.109, F.110, R.114, T.117, W.118, G.121, V.122, L.124, A.125, T.128, I.195, M.199, H.202, F.203, I.206, I.211, S.212 Chain B: L.108 Ligands: HEM.4 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:T.40, A:V.101, A:V.104, A:V.104, A:F.110, A:T.117, A:W.118, A:W.118, A:V.122, A:L.124, A:A.125, A:F.203 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: 26 residues within 4Å: Chain A: K.24, V.26, V.30, N.31, Y.34, C.35, G.38, I.39, L.41, T.42, L.45, F.203, I.206, R.207, G.210, I.211 Chain B: N.25, D.35, V.39, F.40, V.43, I.44 Chain H: V.22, R.26 Ligands: HEM.3, QNO.8 19 PLIP interactions: 11 interactions with chain A, 7 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.30, A:V.30, A:Y.34, A:L.41, A:F.203, A:F.203, A:I.206, A:I.211, 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, B:N.25 Salt bridges: A:R.207 Metal complexes: H2O.1 HEM.14: 35 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, T.8, Y.9, P.13, I.20, V.21, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, V.75, L.115, V.116, P.118, L.119, G.152, A.153, N.154, R.155, G.156, R.157, G.158, Q.159, I.160, Y.161, P.162, S.167 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:Y.1, C:Y.1, C:P.2, C:W.4, C:W.4, C:A.5, C:N.154, C:R.157, C:Y.161, C:Y.161 Hydrogen bonds: C:Y.1, C:N.71, C:G.156 Salt bridges: C:R.157 pi-Stacking: C:W.4 Metal complexes: C:H.26 HEM.19: 29 residues within 4Å: Chain A: F.189 Chain I: F.44, Q.47, F.48, G.51, F.52, M.54, T.55, Y.58, V.69, I.72, R.83, H.86, R.87, A.90, M.93, T.128, F.131, G.132, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192, I.195 Chain J: E.78 17 PLIP interactions: 16 interactions with chain I, 1 interactions with chain A, Hydrophobic interactions: I:F.44, I:Q.47, I:M.54, I:Y.58, I:F.131, I:F.131, I:F.131, I:F.131, I:F.131, I:L.138, I:Y.184, A:F.189 Salt bridges: I:R.83, I:R.83, I:R.87 Metal complexes: I:H.86, I:H.187 HEM.20: 31 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, T.107, G.109, F.110, R.114, T.117, W.118, G.121, V.122, L.124, A.125, T.128, I.195, M.199, H.202, F.203, I.206, I.211, S.212 Chain J: L.108 Ligands: HEM.21 22 PLIP interactions: 22 interactions with chain I, Hydrophobic interactions: I:T.40, I:V.101, I:V.104, I:V.104, I:F.110, I:T.117, I:W.118, I:W.118, I:V.122, I:L.124, I:A.125, I:F.203 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: 26 residues within 4Å: Chain I: K.24, V.26, V.30, N.31, Y.34, C.35, G.38, I.39, L.41, T.42, L.45, F.203, I.206, R.207, G.210, I.211 Chain J: N.25, D.35, V.39, F.40, V.43, I.44 Chain P: V.22, R.26 Ligands: HEM.20, QNO.25 19 PLIP interactions: 11 interactions with chain I, 7 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: I:V.30, I:V.30, I:Y.34, I:L.41, I:F.203, I:F.203, I:I.206, I:I.211, 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, J:N.25 Salt bridges: I:R.207 Metal complexes: H2O.1 HEM.31: 35 residues within 4Å: Chain K: Y.1, P.2, W.4, A.5, T.8, Y.9, P.13, I.20, V.21, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, V.75, L.115, V.116, P.118, L.119, G.152, A.153, N.154, R.155, G.156, R.157, G.158, Q.159, I.160, Y.161, P.162, S.167 16 PLIP interactions: 16 interactions with chain K, Hydrophobic interactions: K:Y.1, K:Y.1, K:P.2, K:W.4, K:W.4, K:A.5, K:N.154, K:R.157, K:Y.161, K:Y.161 Hydrogen bonds: K:Y.1, K:N.71, K:G.156 Salt bridges: K:R.157 pi-Stacking: 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: 34 residues within 4Å: Chain A: I.39, C.43, M.92, M.96 Chain B: T.47, C.50, I.51, L.54 Chain C: P.37, Q.38 Chain E: M.1, G.4, A.5, Y.8, I.9 Chain F: E.3, E.4, Y.7, A.8, L.11, S.12, G.14, L.15, V.18 Chain G: L.5, L.9, L.13 Chain H: V.5, W.8, V.9, L.11, L.12, F.15 Ligands: BCR.17 21 PLIP interactions: 6 interactions with chain H, 7 interactions with chain F, 1 interactions with chain C, 1 interactions with chain A, 3 interactions with chain G, 3 interactions with chain E Hydrophobic interactions: H:W.8, H:W.8, H:L.11, H:L.12, H:F.15, H:F.15, F:Y.7, F:Y.7, F:A.8, F:L.11, F:L.11, F:V.18, A:M.92, G:L.5, G:L.9, G:L.9, E:Y.8, E:Y.8, E:I.9 Salt bridges: F:E.3 Hydrogen bonds: C:Q.38 OPC.12: 24 residues within 4Å: Chain A: Y.105 Chain B: I.87, V.91, L.96, L.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, V.117, N.118, F.120, R.125, R.126, P.127, V.128, A.129, I.132, V.139, L.143 Ligands: CLA.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.100, B:V.111, B:I.114, B:I.132 Hydrogen bonds: B:N.118, B:V.128, B:A.129 OPC.22: 34 residues within 4Å: Chain I: I.39, C.43, M.92, M.96 Chain J: T.47, C.50, I.51, L.54 Chain K: P.37, Q.38 Chain M: M.1, G.4, A.5, Y.8, I.9 Chain N: E.3, E.4, Y.7, A.8, L.11, S.12, G.14, L.15, V.18 Chain O: L.5, L.9, L.13 Chain P: V.5, W.8, V.9, L.11, L.12, F.15 Ligands: BCR.34 21 PLIP interactions: 7 interactions with chain N, 6 interactions with chain P, 1 interactions with chain K, 3 interactions with chain O, 3 interactions with chain M, 1 interactions with chain I Hydrophobic interactions: N:Y.7, N:Y.7, N:A.8, N:L.11, N:L.11, N:V.18, P:W.8, P:W.8, P:L.11, P:L.12, P:F.15, P:F.15, O:L.5, O:L.9, O:L.9, M:Y.8, M:Y.8, M:I.9, I:M.92 Salt bridges: N:E.3 Hydrogen bonds: K:Q.38 OPC.29: 24 residues within 4Å: Chain I: Y.105 Chain J: I.87, V.91, L.96, L.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, V.117, N.118, F.120, R.125, R.126, P.127, V.128, A.129, I.132, V.139, L.143 Ligands: CLA.28 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:L.100, J:V.111, J:I.114, J:I.132 Hydrogen bonds: J:N.118, J:V.128, J:A.129

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

UMQ.6: 14 residues within 4Å: Chain A: D.20, K.24, L.116, L.201, L.204, M.205, R.207, K.208 Chain I: F.8, L.12, I.14, A.16, L.17 Ligands: UMQ.24 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain I Hydrogen bonds: A:D.20, A:D.20, A:K.24, A:K.208 Salt bridges: A:K.208, A:K.208 Hydrophobic interactions: I:L.12, I:L.12 UMQ.7: 9 residues within 4Å: Chain A: N.3, Y.5, D.6, I.14, Q.15, L.17, A.18 Ligands: UMQ.9, UMQ.23 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.5, A:I.14 Hydrogen bonds: A:Q.15 UMQ.9: 12 residues within 4Å: Chain A: Q.15, L.17, A.18, D.19, V.21, T.22 Chain B: W.32 Chain C: E.286 Chain D: R.16 Ligands: UMQ.7, QNO.8, SQD.16 7 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:A.18, A:V.21, A:T.22, B:W.32 Hydrogen bonds: A:Q.15, C:E.286, B:W.32 UMQ.13: 20 residues within 4Å: Chain A: M.73, N.74, E.75, V.76, S.77, F.78, W.80, L.81 Chain B: F.48, V.52, V.56 Chain C: D.251, N.253, R.254, W.257, M.258, F.261 Chain D: G.33, A.34, P.37 10 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:E.75, A:F.78, A:W.80, C:D.251, C:N.253 Hydrophobic interactions: B:F.48, B:V.52, C:F.261, C:F.261, D:P.37 UMQ.23: 14 residues within 4Å: Chain A: F.8, L.12, I.14, A.16, L.17 Chain I: D.20, K.24, L.116, L.201, L.204, M.205, R.207, K.208 Ligands: UMQ.7 8 PLIP interactions: 6 interactions with chain I, 2 interactions with chain A Hydrogen bonds: I:D.20, I:D.20, I:K.24, I:K.208 Salt bridges: I:K.208, I:K.208 Hydrophobic interactions: A:L.12, A:L.12 UMQ.24: 9 residues within 4Å: Chain I: N.3, Y.5, D.6, I.14, Q.15, L.17, A.18 Ligands: UMQ.6, UMQ.26 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:Y.5, I:I.14 Hydrogen bonds: I:Q.15 UMQ.26: 12 residues within 4Å: Chain I: Q.15, L.17, A.18, D.19, V.21, T.22 Chain J: W.32 Chain K: E.286 Chain L: R.16 Ligands: UMQ.24, QNO.25, SQD.33 7 PLIP interactions: 4 interactions with chain I, 1 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: I:A.18, I:V.21, I:T.22, J:W.32 Hydrogen bonds: I:Q.15, K:E.286, J:W.32 UMQ.30: 20 residues within 4Å: Chain I: M.73, N.74, E.75, V.76, S.77, F.78, W.80, L.81 Chain J: F.48, V.52, V.56 Chain K: D.251, N.253, R.254, W.257, M.258, F.261 Chain L: G.33, A.34, P.37 10 PLIP interactions: 4 interactions with chain K, 3 interactions with chain I, 2 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: K:F.261, K:F.261, J:F.48, J:V.52, L:P.37 Hydrogen bonds: K:D.251, K:N.253, I:E.75, I:F.78, I:W.80

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

QNO.8: 12 residues within 4Å: Chain A: K.24, Y.25, V.26, R.207 Chain B: A.31, W.32, L.36, L.37, F.40, P.41 Ligands: HEM.4, UMQ.9 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:L.36, B:F.40 QNO.25: 12 residues within 4Å: Chain I: K.24, Y.25, V.26, R.207 Chain J: A.31, W.32, L.36, L.37, F.40, P.41 Ligands: HEM.21, UMQ.26 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:A.31, J:L.36, J:F.40 Hydrogen bonds: I:R.207, I:R.207

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.11: 33 residues within 4Å: Chain A: M.97, I.98, V.101, F.102, Y.105, W.118, V.122, I.123, A.125, V.126, V.129 Chain B: Y.80, L.81, P.83, V.84, I.87, M.101, A.102, V.104, P.105, L.106, L.108, I.109, V.111, E.115, I.132, F.133, F.135, G.136, V.139, T.140, L.143 Ligands: OPC.12 18 PLIP interactions: 6 interactions with chain A, 11 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:V.84, B:I.87, B:M.101, B:V.104, B:V.104, B:P.105, B:L.108, B:I.132, B:F.133, B:F.133 Water bridges: B:V.84 Metal complexes: H2O.1 CLA.28: 33 residues within 4Å: Chain I: M.97, I.98, V.101, F.102, Y.105, W.118, V.122, I.123, A.125, V.126, V.129 Chain J: Y.80, L.81, P.83, V.84, I.87, M.101, A.102, V.104, P.105, L.106, L.108, I.109, V.111, E.115, I.132, F.133, F.135, G.136, V.139, T.140, L.143 Ligands: OPC.29 18 PLIP interactions: 11 interactions with chain J, 6 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:V.84, J:I.87, J:M.101, J:V.104, J:V.104, J:P.105, J:L.108, J:I.132, J:F.133, J:F.133, I:V.101, I:F.102, I:Y.105, I:Y.105, I:I.123, I:V.129 Water bridges: J:V.84 Metal complexes: H2O.1

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

FES.15: 12 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, P.143, A.144 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.108, D:H.110, D:C.126, D:H.129 FES.32: 12 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, P.143, A.144 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.108, L:H.110, L:C.126, L:H.129

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

SQD.16: 18 residues within 4Å: Chain B: W.32, P.33, L.37, Y.38 Chain C: L.264, K.275, Q.278, V.279 Chain D: R.16, N.20, L.21, L.22, F.24, G.25, T.26, T.28, G.29 Ligands: UMQ.9 8 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: D:F.24, D:T.28, B:L.37 Hydrogen bonds: D:N.20, B:W.32, B:Y.38 Salt bridges: D:R.16, C:K.275 SQD.33: 18 residues within 4Å: Chain J: W.32, P.33, L.37, Y.38 Chain K: L.264, K.275, Q.278, V.279 Chain L: R.16, N.20, L.21, L.22, F.24, G.25, T.26, T.28, G.29 Ligands: UMQ.26 8 PLIP interactions: 3 interactions with chain J, 4 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: J:L.37, L:F.24, L:T.28 Hydrogen bonds: J:W.32, J:Y.38, L:N.20 Salt bridges: L:R.16, K:K.275

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

BCR.17: 26 residues within 4Å: Chain A: I.32, F.33, C.35, L.36, I.39, M.96, L.99 Chain B: V.43, G.46, T.47, C.50 Chain F: I.16, F.17, W.20 Chain G: L.13, A.16, T.17, G.19, G.20, Y.23, Y.26 Chain H: F.15, S.18, I.19, V.22 Ligands: OPC.5 14 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B, 5 interactions with chain A, 1 interactions with chain H, 3 interactions with chain G Hydrophobic interactions: F:I.16, F:I.16, F:F.17, F:F.17, B:V.43, A:I.32, A:F.33, A:F.33, A:I.39, A:L.99, H:F.15, G:L.13, G:Y.23, G:Y.23 BCR.34: 26 residues within 4Å: Chain I: I.32, F.33, C.35, L.36, I.39, M.96, L.99 Chain J: V.43, G.46, T.47, C.50 Chain N: I.16, F.17, W.20 Chain O: L.13, A.16, T.17, G.19, G.20, Y.23, Y.26 Chain P: F.15, S.18, I.19, V.22 Ligands: OPC.22 14 PLIP interactions: 5 interactions with chain I, 4 interactions with chain N, 3 interactions with chain O, 1 interactions with chain P, 1 interactions with chain J Hydrophobic interactions: I:I.32, I:F.33, I:F.33, I:I.39, I:L.99, N:I.16, N:I.16, N:F.17, N:F.17, O:L.13, O:Y.23, O:Y.23, P:F.15, J:V.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasan, S.S. et al., Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-02-13

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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