SMTL ID : 2d2c.1

Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. Laminosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

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

Ligands

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

HEM.1: 23 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, F.131, G.132, G.135, Y.136, L.138, P.139, H.187, T.188 Chain I: F.189 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain I, Hydrophobic interactions: A:F.44, A:Q.47, A:M.54, A:T.55, A:F.131, A:F.131, A:L.138, I:F.189 Salt bridges: A:R.83, A:R.83 pi-Stacking: A:H.86, A:H.86, A:H.187, A:H.187 Metal complexes: A:H.86, A:H.187 HEM.2: 24 residues within 4Å: Chain A: G.37, G.38, T.40, L.41, M.97, H.100, V.101, R.103, V.104, G.108, G.109, T.117, W.118, G.121, V.122, L.124, A.125, T.128, M.199, H.202, F.203, I.206, Q.209 Ligands: HEC.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:T.40, A:V.101, A:V.104, A:V.104, A:W.118, A:W.118, A:W.118, A:L.124, A:L.124, A:A.125, A:F.203, A:I.206 Hydrogen bonds: A:G.38 Salt bridges: A:R.103 pi-Stacking: A:H.100, A:H.100, A:H.202, A:H.202, A:H.202 Metal complexes: A:H.100 HEM.8: 19 residues within 4Å: Chain C: Y.1, P.2, W.4, V.21, C.22, C.25, H.26, Q.60, N.71, V.72, G.73, A.74, 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:V.21, C:H.26, C:N.154, C:Y.161 Hydrogen bonds: C:Q.60, C:N.71, C:N.71, C:G.156 Salt bridges: C:R.157 pi-Stacking: C:Y.1, C:Y.1, C:W.4, C:W.4, C:H.26 HEM.11: 23 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, F.131, G.135, Y.136, L.138, P.139, H.187, T.188 Chain J: M.61 18 PLIP interactions: 17 interactions with chain I, 1 interactions with chain A, Hydrophobic interactions: I:F.44, I:Q.47, I:M.54, I:T.55, I:Y.58, I:F.131, I:F.131, I:F.131, I:L.138, A:F.189 Salt bridges: I:R.83, I:R.83 pi-Stacking: I:H.86, I:H.86, I:H.187, I:H.187 Metal complexes: I:H.86, I:H.187 HEM.12: 25 residues within 4Å: Chain I: Y.34, C.35, G.37, G.38, T.40, L.41, H.100, V.101, R.103, V.104, G.109, R.114, W.118, G.121, V.122, L.124, A.125, T.128, M.199, H.202, F.203, I.206, Q.209, G.210 Ligands: HEC.13 18 PLIP interactions: 18 interactions with chain I, Hydrophobic interactions: I:T.40, I:L.41, I:V.101, I:V.104, I:L.124, I:L.124, I:A.125, I:F.203, I:I.206 Hydrogen bonds: I:G.38 Salt bridges: I:R.103, I:R.114 pi-Stacking: I:H.100, I:H.202, I:H.202, I:H.202, I:H.202 Metal complexes: I:H.100 HEM.18: 19 residues within 4Å: Chain K: Y.1, P.2, W.4, V.21, C.22, C.25, H.26, Q.60, N.71, V.72, G.73, A.74, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 17 PLIP interactions: 17 interactions with chain K, Hydrophobic interactions: K:Y.1, K:P.2, K:V.21, K:H.26, K:N.154, K:Y.161 Hydrogen bonds: K:Q.60, K:N.71, K:N.71, K:G.156, K:Y.161 Salt bridges: K:R.157 pi-Stacking: K:Y.1, K:Y.1, K:W.4, K:W.4, K:H.26

2 x HEC: HEME C(Covalent)

HEC.3: 11 residues within 4Å: Chain A: Y.34, C.35, G.38, T.42, R.207, K.208 Chain B: E.29, F.40, V.43, I.44 Ligands: HEM.2 10 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:F.40, B:F.40, B:V.43, B:V.43, B:I.44, B:I.44 Hydrogen bonds: B:E.29, A:P.27, A:K.208 Metal complexes: H2O.1 HEC.13: 11 residues within 4Å: Chain I: C.35, G.38, L.41, T.42, F.203, I.206 Chain J: F.40, V.43, I.44 Ligands: HEM.12, OPC.14 12 PLIP interactions: 7 interactions with chain J, 4 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:F.40, J:F.40, J:V.43, J:V.43, J:I.44, J:I.44, I:L.41, I:L.41, I:F.203, I:F.203 pi-Stacking: J:F.40 Metal complexes: H2O.1

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.4: 4 residues within 4Å: Chain B: L.37, P.41, I.44 Ligands: OPC.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.37 OPC.7: 5 residues within 4Å: Chain B: Y.38 Chain C: K.275 Chain D: Q.17, N.20 Ligands: OPC.4 No protein-ligand interaction detected (PLIP) OPC.14: 7 residues within 4Å: Chain I: L.41, T.42, L.45, I.46 Chain J: L.37 Ligands: HEC.13, OPC.15 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:T.42 Hydrophobic interactions: J:L.37 OPC.15: 3 residues within 4Å: Chain J: Y.38 Chain K: K.275 Ligands: OPC.14 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I, 1 interactions with chain K Hydrophobic interactions: J:Y.38 Salt bridges: I:K.24, K:K.275

2 x BNT: 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE(Non-covalent)

BNT.5: 10 residues within 4Å: Chain A: D.141, V.143 Chain B: M.61, G.63, E.64, P.65 Chain C: K.146, Y.147, A.148, E.246 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:E.64 Hydrophobic interactions: C:A.148, A:V.143 BNT.16: 10 residues within 4Å: Chain I: V.143 Chain J: M.61, V.62, G.63, E.64, E.74 Chain K: K.146, Y.147, A.148, E.246 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: I:V.143, J:V.62, K:A.148

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.6: 14 residues within 4Å: Chain A: V.101, V.129 Chain B: Y.80, P.83, V.84, I.87, L.100, V.104, P.105, L.106, I.132, F.133, G.136, T.140 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:P.83, B:P.83, B:V.84, B:I.87, B:L.100, B:V.104, B:P.105, B:L.106, B:F.133, B:F.133, A:V.101 Hydrogen bonds: B:V.84 CLA.17: 15 residues within 4Å: Chain I: V.101, F.102, Y.105, A.125 Chain J: Y.80, P.83, V.84, M.101, V.104, P.105, A.129, I.132, F.133, G.136, T.140 11 PLIP interactions: 8 interactions with chain J, 3 interactions with chain I, Hydrophobic interactions: J:V.84, J:V.104, J:V.104, J:V.104, J:V.104, J:I.132, J:F.133, J:F.133, I:V.101, I:F.102, I:Y.105

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

FES.9: 10 residues within 4Å: Chain D: C.108, H.110, L.111, G.112, C.113, V.115, C.126, H.129, S.131, P.143 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.108, D:H.110, D:C.126, D:H.129 FES.19: 10 residues within 4Å: Chain L: C.108, H.110, L.111, G.112, C.113, V.115, C.126, H.129, S.131, P.143 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.108, L:H.110, L:C.126, L:H.129

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

BCR.10: 15 residues within 4Å: Chain A: F.33, I.39, L.99 Chain B: G.46 Chain E: A.13, L.14, F.16, G.17, I.22 Chain F: I.16, F.17, W.20 Chain G: A.24, A.25, Q.28 10 PLIP interactions: 1 interactions with chain G, 3 interactions with chain A, 3 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: G:A.24, A:F.33, A:I.39, A:L.99, F:I.16, F:F.17, F:W.20, E:L.14, E:F.16, E:F.16 BCR.20: 15 residues within 4Å: Chain I: F.33, I.39 Chain J: V.43, G.46, T.47 Chain M: A.13, F.16, G.17, I.22 Chain N: I.16, F.17, W.20 Chain O: A.24, A.25, Q.28 9 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I, 2 interactions with chain M, 3 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: J:T.47, I:F.33, I:I.39, M:F.16, M:F.16, N:I.16, N:F.17, N:W.20, O:A.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, J. et al., Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex. Proc.Natl.Acad.Sci.USA (2006)

Release Date

2005-12-13

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 VI: EM
Cytochrome b6-f complex subunit VII: FN
Cytochrome b6-f complex subunit V: GO
Cytochrome b6-f complex subunit VIII: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

I
N

B
B

J
O

C
C

K
P

D
D

L
Q

E
E

M
R

F
F

N
S

G
G

O
T

H
H

P
U

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 VI

Cytochrome b6-f complex subunit VII

Cytochrome b6-f complex subunit V

Cytochrome b6-f complex subunit VIII

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