SMTL ID : 4i7z.1

Crystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein soluble domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

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

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: F.44, Q.47, F.48, G.51, F.52, M.54, T.55, Y.58, V.69, 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 Chain B: A.60 Chain I: F.189 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Q.47, A:F.48, A:M.54, A:T.55, A:Y.58, A:R.87, A:A.90, A:T.128, A:F.131, A:F.131, A:F.131, A:F.131, A:L.138, A:Y.184, A:T.188, A:P.192 Salt bridges: A:R.83, A:R.83 Metal complexes: A:H.86, A:H.187 HEM.2: 29 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, F.110, R.114, T.117, W.118, G.121, V.122, L.124, A.125, I.195, M.199, H.202, F.203, I.206, G.210, I.211, S.212 Ligands: HEM.3 20 PLIP interactions: 20 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:A.125 Hydrogen bonds: A:G.37, A:G.38, A:S.212 Water bridges: A:H.100, A:R.103, A:R.103 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 Metal complexes: A:H.100, A:H.202 HEM.3: 21 residues within 4Å: Chain A: K.24, V.26, 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, D.35, V.39, F.40, V.43, I.44 Chain H: R.26 Ligands: HEM.2 14 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:V.39, B:F.40, B:F.40, B:F.40, B:I.44, B:I.44, A:Y.34, A:L.41, A:I.206 Hydrogen bonds: B:N.25, A:I.211 Salt bridges: A:R.207, A:R.207 Metal complexes: H2O.1 HEM.13: 26 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, T.8, Y.9, V.21, C.22, C.25, H.26, Q.60, A.63, L.70, N.71, V.72, G.73, A.74, V.75, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:Y.1, C:P.2, C:W.4, C:W.4, C:N.71, C:R.157, C:Y.161, C:Y.161 Hydrogen bonds: C:Q.60, C:N.71, C:N.71, C:N.71, C:Y.161 Salt bridges: C:R.157 pi-Stacking: C:W.4 Metal complexes: C:H.26 HEM.20: 27 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, 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 Chain J: A.60 20 PLIP interactions: 20 interactions with chain I, Hydrophobic interactions: I:Q.47, I:F.48, I:M.54, I:T.55, I:Y.58, I:R.87, I:A.90, I:T.128, I:F.131, I:F.131, 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 Metal complexes: I:H.86, I:H.187 HEM.21: 29 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, F.110, R.114, T.117, W.118, G.121, V.122, L.124, A.125, I.195, M.199, H.202, F.203, I.206, G.210, I.211, S.212 Ligands: HEM.22 20 PLIP interactions: 20 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:A.125 Hydrogen bonds: I:G.37, I:G.38, I:S.212 Water bridges: I:H.100, I:R.103, I:R.103 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 Metal complexes: I:H.100, I:H.202 HEM.22: 21 residues within 4Å: Chain I: K.24, V.26, 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, D.35, V.39, F.40, V.43, I.44 Chain P: R.26 Ligands: HEM.21 14 PLIP interactions: 6 interactions with chain I, 7 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: I:Y.34, I:L.41, I:I.206, J:V.39, J:F.40, J:F.40, J:F.40, J:I.44, J:I.44 Hydrogen bonds: I:I.211, J:N.25 Salt bridges: I:R.207, I:R.207 Metal complexes: H2O.1 HEM.32: 26 residues within 4Å: Chain K: Y.1, P.2, W.4, A.5, T.8, Y.9, V.21, C.22, C.25, H.26, Q.60, A.63, L.70, N.71, V.72, G.73, A.74, V.75, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 16 PLIP interactions: 16 interactions with chain K, Hydrophobic interactions: K:Y.1, K:P.2, K:W.4, K:W.4, K:N.71, K:R.157, K:Y.161, K:Y.161 Hydrogen bonds: K:Q.60, K:N.71, K:N.71, K:N.71, K:Y.161 Salt bridges: K:R.157 pi-Stacking: K:W.4 Metal complexes: K:H.26

2 x MYS: PENTADECANE(Non-covalent)

MYS.4: 15 residues within 4Å: Chain A: V.126, I.127, V.129, S.130, V.133, T.134, L.169, R.182, Y.183, A.186, V.190, L.191, L.194 Chain I: F.56 Ligands: CLA.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.134, A:A.186 MYS.23: 15 residues within 4Å: Chain A: F.56 Chain I: V.126, I.127, V.129, S.130, V.133, T.134, L.169, R.182, Y.183, A.186, V.190, L.191, L.194 Ligands: CLA.29 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:T.134, I:A.186

2 x 8K6: Octadecane(Non-covalent)

8K6.5: 16 residues within 4Å: Chain A: L.41, F.44, L.45, F.48, A.49, F.52, A.196, M.199, L.200, F.203 Chain D: L.38 Chain I: F.189, V.190, W.193, L.194, V.197 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: A:F.48, A:F.48, A:F.52, A:F.52, A:M.199, A:F.203, I:W.193, I:L.194 8K6.24: 16 residues within 4Å: Chain A: F.189, V.190, W.193, L.194, V.197 Chain I: L.41, F.44, L.45, F.48, A.49, F.52, A.196, M.199, L.200, F.203 Chain L: L.38 8 PLIP interactions: 6 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: I:F.48, I:F.48, I:F.52, I:F.52, I:M.199, I:F.203, A:W.193, A:L.194

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

UMQ.6: 17 residues within 4Å: Chain A: L.116, I.119, S.120, I.123, F.198, L.201, L.204, M.205, R.207, K.208 Chain I: F.8, L.12, E.13, I.14, A.16, L.17 Ligands: UMQ.26 7 PLIP interactions: 3 interactions with chain I, 4 interactions with chain A Hydrogen bonds: I:L.12, I:L.12, I:E.13, A:K.208 Hydrophobic interactions: A:I.119 Salt bridges: A:K.208, A:K.208 UMQ.7: 10 residues within 4Å: Chain A: N.3, Y.5, D.6, I.14, Q.15, L.17, A.18 Chain I: L.201 Ligands: UMQ.8, UMQ.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.14, A:I.14, A:A.18 Hydrogen bonds: A:Q.15 UMQ.8: 11 residues within 4Å: Chain A: Q.15, A.18, V.21, T.22 Chain B: W.32, P.33 Chain C: V.279, Q.283, E.286 Ligands: UMQ.7, 1E2.16 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:E.286, B:W.32, A:Q.15 Hydrophobic interactions: B:W.32 UMQ.25: 17 residues within 4Å: Chain A: F.8, L.12, E.13, I.14, A.16, L.17 Chain I: L.116, I.119, S.120, I.123, F.198, L.201, L.204, M.205, R.207, K.208 Ligands: UMQ.7 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain I Hydrogen bonds: A:L.12, A:L.12, A:E.13, I:K.208 Hydrophobic interactions: I:I.119 Salt bridges: I:K.208, I:K.208 UMQ.26: 10 residues within 4Å: Chain A: L.201 Chain I: N.3, Y.5, D.6, I.14, Q.15, L.17, A.18 Ligands: UMQ.6, UMQ.27 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:I.14, I:I.14, I:A.18 Hydrogen bonds: I:Q.15 UMQ.27: 11 residues within 4Å: Chain I: Q.15, A.18, V.21, T.22 Chain J: W.32, P.33 Chain K: V.279, Q.283, E.286 Ligands: UMQ.26, 1E2.35 4 PLIP interactions: 1 interactions with chain I, 2 interactions with chain J, 1 interactions with chain K Hydrogen bonds: I:Q.15, J:W.32, K:E.286 Hydrophobic interactions: J:W.32

6 x CD: CADMIUM ION(Non-covalent)

CD.9: 4 residues within 4Å: Chain A: N.74, E.75 Chain C: K.140, H.143 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:E.75, C:H.143, H2O.1 CD.11: 6 residues within 4Å: Chain B: D.58 Chain C: K.146 Chain F: E.4 Chain G: E.3, P.4, L.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Metal complexes: B:D.58, F:E.4 CD.14: 2 residues within 4Å: Chain C: A.148, H.150 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.150 CD.28: 4 residues within 4Å: Chain I: N.74, E.75 Chain K: K.140, H.143 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: I:E.75, K:H.143, H2O.1 CD.30: 6 residues within 4Å: Chain J: D.58 Chain K: K.146 Chain N: E.4 Chain O: E.3, P.4, L.5 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain N Metal complexes: J:D.58, N:E.4 CD.33: 2 residues within 4Å: Chain K: A.148, H.150 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:H.150

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.10: 35 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: W.79, 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, A.129, I.132, F.133, F.135, G.136, V.139, T.140, L.143 Ligands: MYS.4, OZ2.12 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:L.108, B:I.132, B:F.133, B:V.139 Hydrogen bonds: B:V.84 Metal complexes: H2O.1 CLA.29: 35 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: W.79, 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, A.129, I.132, F.133, F.135, G.136, V.139, T.140, L.143 Ligands: MYS.23, OZ2.31 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:L.108, J:I.132, J:F.133, J:V.139 Hydrogen bonds: J:V.84 Metal complexes: H2O.1

6 x OZ2: (2R)-3-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6Z)-tridec-6-enoyloxy]propyl (9Z)-octadec-9-enoate(Non-covalent)

OZ2.12: 20 residues within 4Å: Chain A: Y.105, K.111 Chain B: I.87, L.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, N.118, F.120, R.125, R.126, P.127, V.128, A.129, I.132 Ligands: CLA.10 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Y.105, B:N.118, B:R.126, B:V.128, B:A.129 Hydrophobic interactions: B:L.108, B:V.111, B:I.114 OZ2.15: 19 residues within 4Å: Chain A: V.76, S.77, F.78, W.80, L.81 Chain B: F.48, V.52, V.56 Chain C: N.253, R.254, W.257, M.258, A.260, F.261, L.264 Chain D: G.33, A.34, Y.36, P.37 11 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:F.78, A:W.80, A:L.81, B:V.52, C:R.254, C:W.257, C:F.261, D:Y.36, D:Y.36 Hydrogen bonds: A:F.78, A:W.80 OZ2.19: 29 residues within 4Å: Chain A: C.43, M.92, M.96 Chain B: T.47, C.50, L.54 Chain C: V.36, P.37, Q.38, S.39 Chain E: G.4, A.5, Y.8, I.9 Chain F: E.4, Y.7, A.8, L.11, S.12, L.15 Chain G: L.5, L.9, L.13 Chain H: V.5, W.8, L.11, L.12, F.15 Ligands: BCR.18 14 PLIP interactions: 3 interactions with chain F, 2 interactions with chain G, 5 interactions with chain H, 1 interactions with chain C, 1 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: F:Y.7, F:Y.7, F:L.11, G:L.5, G:L.9, H:W.8, H:L.12, H:F.15, H:F.15, H:F.15, A:M.92, E:Y.8, E:I.9 Hydrogen bonds: C:Q.38 OZ2.31: 20 residues within 4Å: Chain I: Y.105, K.111 Chain J: I.87, L.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, N.118, F.120, R.125, R.126, P.127, V.128, A.129, I.132 Ligands: CLA.29 8 PLIP interactions: 1 interactions with chain I, 7 interactions with chain J Hydrogen bonds: I:Y.105, J:N.118, J:R.126, J:V.128, J:A.129 Hydrophobic interactions: J:L.108, J:V.111, J:I.114 OZ2.34: 19 residues within 4Å: Chain I: V.76, S.77, F.78, W.80, L.81 Chain J: F.48, V.52, V.56 Chain K: N.253, R.254, W.257, M.258, A.260, F.261, L.264 Chain L: G.33, A.34, Y.36, P.37 11 PLIP interactions: 3 interactions with chain K, 5 interactions with chain I, 2 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: K:R.254, K:W.257, K:F.261, I:F.78, I:W.80, I:L.81, L:Y.36, L:Y.36, J:V.52 Hydrogen bonds: I:F.78, I:W.80 OZ2.38: 29 residues within 4Å: Chain I: C.43, M.92, M.96 Chain J: T.47, C.50, L.54 Chain K: V.36, P.37, Q.38, S.39 Chain M: G.4, A.5, Y.8, I.9 Chain N: E.4, Y.7, A.8, L.11, S.12, L.15 Chain O: L.5, L.9, L.13 Chain P: V.5, W.8, L.11, L.12, F.15 Ligands: BCR.37 14 PLIP interactions: 2 interactions with chain M, 5 interactions with chain P, 1 interactions with chain K, 3 interactions with chain N, 1 interactions with chain I, 2 interactions with chain O Hydrophobic interactions: M:Y.8, M:I.9, P:W.8, P:L.12, P:F.15, P:F.15, P:F.15, N:Y.7, N:Y.7, N:L.11, I:M.92, O:L.5, O:L.9 Hydrogen bonds: K:Q.38

2 x 1E2: (2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside(Non-covalent)

1E2.16: 11 residues within 4Å: Chain B: W.32, P.33, L.37, Y.38 Chain C: K.275, Q.278, V.279 Chain D: R.16, N.20, F.24 Ligands: UMQ.8 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:F.24 Hydrogen bonds: D:N.20, B:W.32 Salt bridges: D:R.16, C:K.275 1E2.35: 11 residues within 4Å: Chain J: W.32, P.33, L.37, Y.38 Chain K: K.275, Q.278, V.279 Chain L: R.16, N.20, F.24 Ligands: UMQ.27 5 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L, 1 interactions with chain J Salt bridges: K:K.275, L:R.16 Hydrophobic interactions: L:F.24 Hydrogen bonds: L:N.20, J:W.32

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

OCT.17: 6 residues within 4Å: Chain F: F.17, W.20, G.21, V.24 Chain G: Y.23 Ligands: BCR.18 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.17, F:W.20, F:V.24 OCT.36: 6 residues within 4Å: Chain N: F.17, W.20, G.21, V.24 Chain O: Y.23 Ligands: BCR.37 3 PLIP interactions: 3 interactions with chain N Hydrophobic interactions: N:F.17, N:W.20, N:V.24

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

BCR.18: 25 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 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, V.22 Ligands: OCT.17, OZ2.19 14 PLIP interactions: 7 interactions with chain A, 3 interactions with chain F, 2 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: A:I.32, A:I.32, A:I.32, A:F.33, A:F.33, A:I.39, A:L.99, F:I.16, F:F.17, F:F.17, H:I.19, H:V.22, G:Y.23, G:Y.23 BCR.37: 25 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 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, V.22 Ligands: OCT.36, OZ2.38 14 PLIP interactions: 7 interactions with chain I, 2 interactions with chain P, 3 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: I:I.32, I:I.32, I:I.32, I:F.33, I:F.33, I:I.39, I:L.99, P:I.19, P:V.22, N:I.16, N:F.17, N:F.17, O:Y.23, O:Y.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasan, S.S. et al., Lipid-induced conformational changes within the cytochrome b6f complex of oxygenic photosynthesis. Biochemistry (2013)

Release Date

2013-04-17

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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