SMTL ID : 1q90.1 (1 other biounit)

Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

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

Ligands

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

HEC.1: 24 residues within 4Å: Chain A: Y.1, P.2, F.4, A.5, Y.9, V.20, C.21, C.24, H.25, Q.59, A.62, L.69, N.70, V.71, G.72, M.73, P.117, N.153, G.155, R.156, G.157, V.159, Y.160, P.161 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:Y.1, A:Y.1, A:Y.1, A:P.2, A:F.4, A:A.5, A:Y.9, A:N.70, A:P.117, A:R.156, A:R.156, A:Y.160, A:P.161 Hydrogen bonds: A:Y.1, A:Q.59, A:N.70, A:N.70, A:G.155, A:Y.160 Salt bridges: A:R.156 pi-Stacking: A:Y.1, A:Y.1, A:H.25, A:H.25, A:H.25 Metal complexes: A:H.25 HEC.2: 18 residues within 4Å: Chain B: V.30, N.31, Y.34, C.35, G.38, F.41, T.42, F.203, I.206, R.207, G.210, I.211 Chain D: N.25, F.40, V.43, I.44 Chain I: R.28 Ligands: HEC.3 13 PLIP interactions: 5 interactions with chain D, 7 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: D:V.43, D:I.44, D:I.44, B:V.30, B:F.41, B:F.203, B:I.206, B:I.211 pi-Stacking: D:F.40, D:F.40 Hydrogen bonds: B:I.211 Salt bridges: B:R.207 Metal complexes: H2O.1 HEC.3: 25 residues within 4Å: Chain B: Y.34, G.37, G.38, T.40, F.41, H.100, V.101, R.103, V.104, G.109, F.110, R.114, T.117, W.118, G.121, V.122, M.124, A.125, T.128, M.199, H.202, I.206, I.211, S.212 Ligands: HEC.2 27 PLIP interactions: 27 interactions with chain B, Hydrophobic interactions: B:T.40, B:F.41, B:V.101, B:V.104, B:V.104, B:T.117, B:W.118, B:W.118, B:V.122, B:M.124, B:A.125, B:I.206 Hydrogen bonds: B:G.37, B:G.38, B:S.212 Water bridges: B:Y.34, B:C.35, B:I.36 Salt bridges: B:H.100, B:R.103, B:R.103, B:R.114 pi-Stacking: B:H.100, B:H.100, B:H.202 Metal complexes: B:H.100, B:H.202 HEC.4: 23 residues within 4Å: Chain B: F.44, Q.47, V.48, G.51, F.52, M.54, T.55, V.69, R.83, H.86, R.87, A.90, M.93, F.131, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192 Chain K: F.189 26 PLIP interactions: 25 interactions with chain B, 1 interactions with chain K, Hydrophobic interactions: B:F.44, B:Q.47, B:M.54, B:R.87, B:A.90, B:F.131, B:F.131, B:F.131, B:F.131, B:Y.136, B:Y.136, B:Y.136, B:L.138, B:Y.184, B:T.188, B:P.192, K:F.189 Salt bridges: B:R.83, B:R.83, B:R.87 pi-Stacking: B:H.86, B:H.187, B:H.187, B:H.187 Metal complexes: B:H.86, B:H.187 HEC.13: 24 residues within 4Å: Chain J: Y.1, P.2, F.4, A.5, Y.9, V.20, C.21, C.24, H.25, Q.59, A.62, L.69, N.70, V.71, G.72, M.73, P.117, N.153, G.155, R.156, G.157, V.159, Y.160, P.161 26 PLIP interactions: 26 interactions with chain J, Hydrophobic interactions: J:Y.1, J:Y.1, J:Y.1, J:P.2, J:F.4, J:A.5, J:Y.9, J:N.70, J:P.117, J:R.156, J:R.156, J:Y.160, J:P.161 Hydrogen bonds: J:Y.1, J:Q.59, J:N.70, J:N.70, J:G.155, J:Y.160 Salt bridges: J:R.156 pi-Stacking: J:Y.1, J:Y.1, J:H.25, J:H.25, J:H.25 Metal complexes: J:H.25 HEC.14: 18 residues within 4Å: Chain K: V.30, N.31, Y.34, C.35, G.38, F.41, T.42, F.203, I.206, R.207, G.210, I.211 Chain M: N.25, F.40, V.43, I.44 Chain R: R.28 Ligands: HEC.15 13 PLIP interactions: 5 interactions with chain M, 7 interactions with chain K, 1 Ligand-Water interactions, Hydrophobic interactions: M:V.43, M:I.44, M:I.44, K:V.30, K:F.41, K:F.203, K:I.206, K:I.211 pi-Stacking: M:F.40, M:F.40 Hydrogen bonds: K:I.211 Salt bridges: K:R.207 Metal complexes: H2O.1 HEC.15: 25 residues within 4Å: Chain K: Y.34, G.37, G.38, T.40, F.41, H.100, V.101, R.103, V.104, G.109, F.110, R.114, T.117, W.118, G.121, V.122, M.124, A.125, T.128, M.199, H.202, I.206, I.211, S.212 Ligands: HEC.14 27 PLIP interactions: 27 interactions with chain K, Hydrophobic interactions: K:T.40, K:F.41, K:V.101, K:V.104, K:V.104, K:T.117, K:W.118, K:W.118, K:V.122, K:M.124, K:A.125, K:I.206 Hydrogen bonds: K:G.37, K:G.38, K:S.212 Water bridges: K:Y.34, K:C.35, K:I.36 Salt bridges: K:H.100, K:R.103, K:R.103, K:R.114 pi-Stacking: K:H.100, K:H.100, K:H.202 Metal complexes: K:H.100, K:H.202 HEC.16: 23 residues within 4Å: Chain B: F.189 Chain K: F.44, Q.47, V.48, G.51, F.52, M.54, T.55, V.69, R.83, H.86, R.87, A.90, M.93, F.131, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192 26 PLIP interactions: 25 interactions with chain K, 1 interactions with chain B, Hydrophobic interactions: K:F.44, K:Q.47, K:M.54, K:R.87, K:A.90, K:F.131, K:F.131, K:F.131, K:F.131, K:Y.136, K:Y.136, K:Y.136, K:L.138, K:Y.184, K:T.188, K:P.192, B:F.189 Salt bridges: K:R.83, K:R.83, K:R.87 pi-Stacking: K:H.86, K:H.187, K:H.187, K:H.187 Metal complexes: K:H.86, K:H.187

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

BCR.5: 18 residues within 4Å: Chain B: I.32, F.33, I.39, M.96, L.99 Chain D: V.43, T.47 Chain F: L.13, V.16, A.19, G.20, V.23 Chain H: T.17, L.21 Chain I: F.17, S.20, L.21 Ligands: LMG.12 14 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D, 2 interactions with chain H, 6 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: F:L.13, F:A.19, F:V.23, D:V.43, H:T.17, H:L.21, B:I.32, B:I.32, B:F.33, B:F.33, B:I.39, B:L.99, I:F.17, I:L.21 BCR.17: 18 residues within 4Å: Chain K: I.32, F.33, I.39, M.96, L.99 Chain M: V.43, T.47 Chain O: L.13, V.16, A.19, G.20, V.23 Chain Q: T.17, L.21 Chain R: F.17, S.20, L.21 Ligands: LMG.24 14 PLIP interactions: 2 interactions with chain R, 3 interactions with chain O, 2 interactions with chain Q, 6 interactions with chain K, 1 interactions with chain M Hydrophobic interactions: R:F.17, R:L.21, O:L.13, O:A.19, O:V.23, Q:T.17, Q:L.21, K:I.32, K:I.32, K:F.33, K:F.33, K:I.39, K:L.99, M:V.43

2 x LFA: EICOSANE(Non-covalent)

LFA.6: 11 residues within 4Å: Chain A: A.250, R.251, G.254, L.255, F.258 Chain B: L.81 Chain D: F.48, I.52 Chain E: L.30, G.33, Y.34 6 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: D:F.48, D:F.48, D:I.52, E:L.30, E:Y.34, A:F.258 LFA.18: 11 residues within 4Å: Chain J: A.250, R.251, G.254, L.255, F.258 Chain K: L.81 Chain M: F.48, I.52 Chain N: L.30, G.33, Y.34 6 PLIP interactions: 3 interactions with chain M, 2 interactions with chain N, 1 interactions with chain J Hydrophobic interactions: M:F.48, M:F.48, M:I.52, N:L.30, N:Y.34, J:F.258

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

FES.7: 10 residues within 4Å: Chain C: C.55, H.57, L.58, G.59, C.60, C.73, C.75, H.76, G.77, S.78 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.55, C:H.57, C:C.73, C:H.76 FES.19: 10 residues within 4Å: Chain L: C.55, H.57, L.58, G.59, C.60, C.73, C.75, H.76, G.77, S.78 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.55, L:H.57, L:C.73, L:H.76

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.8: 22 residues within 4Å: Chain B: M.97, V.98, F.102, Y.105, A.125, V.126, V.129, S.130, V.133 Chain D: Y.80, F.81, P.83, V.84, V.104, L.108, L.132, F.133, G.136, V.139, A.140 Ligands: TDS.9, LMG.10 15 PLIP interactions: 8 interactions with chain D, 7 interactions with chain B, Hydrophobic interactions: D:F.81, D:V.104, D:L.108, D:L.132, D:F.133, D:F.133, D:V.139, D:A.140, B:V.98, B:F.102, B:Y.105, B:Y.105, B:V.126, B:V.129, B:V.133 CLA.20: 22 residues within 4Å: Chain K: M.97, V.98, F.102, Y.105, A.125, V.126, V.129, S.130, V.133 Chain M: Y.80, F.81, P.83, V.84, V.104, L.108, L.132, F.133, G.136, V.139, A.140 Ligands: TDS.21, LMG.22 15 PLIP interactions: 8 interactions with chain M, 7 interactions with chain K, Hydrophobic interactions: M:F.81, M:V.104, M:L.108, M:L.132, M:F.133, M:F.133, M:V.139, M:A.140, K:V.98, K:F.102, K:Y.105, K:Y.105, K:V.126, K:V.129, K:V.133

2 x TDS: 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE(Non-covalent)

TDS.9: 18 residues within 4Å: Chain B: V.143, A.147, I.150, V.151, P.155, I.165 Chain C: C.75, H.76 Chain D: I.75, L.76, P.77, E.78, F.81, V.84, F.85, L.88, M.101 Ligands: CLA.8 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:I.150, B:I.150, B:P.155, B:I.165, D:F.81, D:V.84, D:L.88 TDS.21: 18 residues within 4Å: Chain K: V.143, A.147, I.150, V.151, P.155, I.165 Chain L: C.75, H.76 Chain M: I.75, L.76, P.77, E.78, F.81, V.84, F.85, L.88, M.101 Ligands: CLA.20 7 PLIP interactions: 3 interactions with chain M, 4 interactions with chain K Hydrophobic interactions: M:F.81, M:V.84, M:L.88, K:I.150, K:I.150, K:P.155, K:I.165

4 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.10: 19 residues within 4Å: Chain B: F.102 Chain D: W.79, Y.82, L.134, G.136, T.137, A.140, G.144, I.145, T.148 Chain F: C.7, L.11, P.15, I.18, F.22 Chain H: E.2, A.3, I.6 Ligands: CLA.8 13 PLIP interactions: 7 interactions with chain D, 4 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: D:W.79, D:Y.82, D:L.134, D:T.137, D:A.140, D:I.145, F:L.11, F:P.15, F:I.18, F:F.22, B:F.102, B:F.102 Hydrogen bonds: D:T.148 LMG.12: 24 residues within 4Å: Chain A: Q.37 Chain B: I.39, C.43, M.92, M.96 Chain D: T.47, C.50, L.54 Chain F: L.5 Chain G: T.3, I.4, Y.7 Chain H: F.5, T.9, T.12, M.13, M.16, V.19 Chain I: E.2, Q.7, W.10, C.14, F.17 Ligands: BCR.5 14 PLIP interactions: 3 interactions with chain H, 2 interactions with chain D, 2 interactions with chain B, 3 interactions with chain I, 4 interactions with chain G Hydrophobic interactions: H:T.9, H:V.19, D:T.47, D:L.54, B:I.39, B:M.92, I:W.10, I:F.17, G:Y.7, G:Y.7 Hydrogen bonds: H:T.12, I:Q.7, G:T.3, G:T.3 LMG.22: 19 residues within 4Å: Chain K: F.102 Chain M: W.79, Y.82, L.134, G.136, T.137, A.140, G.144, I.145, T.148 Chain O: C.7, L.11, P.15, I.18, F.22 Chain Q: E.2, A.3, I.6 Ligands: CLA.20 13 PLIP interactions: 4 interactions with chain O, 7 interactions with chain M, 2 interactions with chain K Hydrophobic interactions: O:L.11, O:P.15, O:I.18, O:F.22, M:W.79, M:Y.82, M:L.134, M:T.137, M:A.140, M:I.145, K:F.102, K:F.102 Hydrogen bonds: M:T.148 LMG.24: 24 residues within 4Å: Chain J: Q.37 Chain K: I.39, C.43, M.92, M.96 Chain M: T.47, C.50, L.54 Chain O: L.5 Chain P: T.3, I.4, Y.7 Chain Q: F.5, T.9, T.12, M.13, M.16, V.19 Chain R: E.2, Q.7, W.10, C.14, F.17 Ligands: BCR.17 14 PLIP interactions: 3 interactions with chain R, 2 interactions with chain M, 4 interactions with chain P, 3 interactions with chain Q, 2 interactions with chain K Hydrophobic interactions: R:W.10, R:F.17, M:T.47, M:L.54, P:Y.7, P:Y.7, Q:T.9, Q:V.19, K:I.39, K:M.92 Hydrogen bonds: R:Q.7, P:T.3, P:T.3, Q:T.12

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

SQD.11: 8 residues within 4Å: Chain A: K.272, F.276 Chain D: W.32, L.37 Chain E: R.12, N.16, A.23, I.27 9 PLIP interactions: 5 interactions with chain E, 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: E:A.23, E:I.27, D:L.37 Hydrogen bonds: E:N.16, E:N.16, D:W.32, D:Y.38 Salt bridges: E:R.12, A:K.272 SQD.23: 8 residues within 4Å: Chain J: K.272, F.276 Chain M: W.32, L.37 Chain N: R.12, N.16, A.23, I.27 9 PLIP interactions: 3 interactions with chain M, 5 interactions with chain N, 1 interactions with chain J Hydrophobic interactions: M:L.37, N:A.23, N:I.27 Hydrogen bonds: M:W.32, M:Y.38, N:N.16, N:N.16 Salt bridges: N:R.12, J:K.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroebel, D. et al., An Atypical Haem in the Cytochrome B6F Complex. Nature (2003)

Release Date

2003-12-09

Peptides

Apocytochrome f: AJ
Cytochrome b6: BK
Cytochrome B6-F complex iron-sulfur subunit: CL
Cytochrome b6-f complex subunit 4: DM
Cytochrome B6-F complex iron-sulfur subunit: EN
Cytochrome b6f complex subunit petG: FO
Cytochrome b6f complex subunit petL: GP
Cytochrome b6f complex subunit PETM: HQ
Cytochrome b6f complex subunit PETN: IR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
A

B
B

K
B

C
C

L
C

D
D

M
D

E
R

N
R

F
G

O
G

G
L

P
L

H
M

Q
M

I
N

R
N

Membrane

We predict this structure to be a membrane protein.
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Apocytochrome f

Cytochrome b6

Cytochrome B6-F complex iron-sulfur subunit

Cytochrome b6-f complex subunit 4

Cytochrome B6-F complex iron-sulfur subunit

Cytochrome b6f complex subunit petG

Cytochrome b6f complex subunit petL

Cytochrome b6f complex subunit PETM

Cytochrome b6f complex subunit PETN

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