SMTL ID : 1vf5.1

Crystal Structure of Cytochrome b6f Complex from M.laminosus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

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

HEM.1: 22 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, A.90, M.93, F.131, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188 Chain I: F.189 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain I, Hydrophobic interactions: A:F.44, A:Q.47, A:Q.47, A:M.54, A:T.55, 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 pi-Stacking: A:H.86, A:H.86, A:H.187, A:H.187 Metal complexes: A:H.86, A:H.187 HEM.2: 27 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, R.114, W.118, G.121, V.122, L.124, A.125, T.128, I.195, M.199, H.202, F.203, I.206, K.208, Q.209 Ligands: HEM.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:L.41, A:V.101, A:V.104, A:V.104, A:W.118, A:W.118, A:L.124, A:A.125, A:I.195, A:F.203, A:I.206 Hydrogen bonds: A:G.37 Water bridges: A:G.38 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 pi-Stacking: A:H.202 Metal complexes: A:H.202 HEM.3: 15 residues within 4Å: Chain A: N.31, Y.34, C.35, G.38, L.41, F.203, I.206, R.207, K.208 Chain B: V.39, F.40, V.43, I.44 Ligands: HEM.2, PL9.5 9 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:V.39, B:F.40, B:V.43, B:I.44, A:Y.34, A:L.41 pi-Stacking: B:F.40 Hydrogen bonds: A:K.208 Metal complexes: H2O.1 HEM.8: 22 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, V.21, C.22, C.25, H.26, Q.60, G.69, N.71, V.72, G.73, A.74, L.115, L.119, N.154, G.156, R.157, G.158, I.160, Y.161 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:Y.1, C:P.2, C:A.5, C:L.115, C:L.119, C:R.157, C:Y.161, C:Y.161 Hydrogen bonds: C:Y.1, C:Q.60, C:Q.60, C:N.71, C:N.71, C:G.156, C:Y.161 Salt bridges: C:R.157 pi-Stacking: C:Y.1, C:Y.1, C:W.4, C:H.26, C:H.26 Metal complexes: C:H.26 HEM.12: 22 residues within 4Å: Chain A: F.189 Chain I: F.44, Q.47, F.48, G.51, F.52, M.54, T.55, 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 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:T.55, 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.13: 26 residues within 4Å: Chain I: Y.34, G.37, G.38, T.40, L.41, M.93, M.97, H.100, R.103, V.104, G.109, F.110, R.114, W.118, G.121, V.122, L.124, A.125, T.128, I.195, M.199, H.202, F.203, I.206, G.210 Ligands: HEM.14 19 PLIP interactions: 19 interactions with chain I, Hydrophobic interactions: I:V.104, I:V.104, I:W.118, I:V.122, I:L.124, I:A.125, I:I.195, I:F.203 Hydrogen bonds: I:R.103 Water bridges: I:Y.34, I:G.37 Salt bridges: I:H.100, I:R.103, I:R.114 pi-Stacking: I:H.100, I:H.202, I:H.202, I:H.202 Metal complexes: I:H.202 HEM.14: 15 residues within 4Å: Chain I: Y.34, C.35, G.38, L.41, T.42, F.203, I.206, K.208 Chain J: V.39, F.40, V.43, I.44 Chain O: R.31 Ligands: HEM.13, PL9.19 8 PLIP interactions: 6 interactions with chain J, 1 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:V.39, J:F.40, J:V.43, J:V.43, J:I.44, J:I.44, I:L.41 Metal complexes: H2O.1 HEM.18: 23 residues within 4Å: Chain K: Y.1, P.2, W.4, A.5, V.21, C.22, C.25, H.26, Q.60, G.69, L.70, N.71, V.72, G.73, A.74, L.115, L.119, N.154, G.156, R.157, G.158, I.160, Y.161 22 PLIP interactions: 22 interactions with chain K, Hydrophobic interactions: K:Y.1, K:P.2, K:A.5, K:N.71, K:L.115, K:L.119, K:R.157, K:Y.161, K:Y.161 Hydrogen bonds: K:Y.1, K:Y.1, K:Q.60, K:N.71, K:N.71, K:G.156 Salt bridges: K:R.157 pi-Stacking: K:Y.1, K:Y.1, K:W.4, K:H.26, K:H.26 Metal complexes: K:H.26

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

TDS.4: 13 residues within 4Å: Chain A: S.130, V.133, T.134, V.151, L.169, Y.183, A.186, V.190 Chain B: L.81, F.85, L.88 Ligands: CLA.7, OPC.16 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.133, A:V.151, A:Y.183, B:L.81, B:F.85, B:F.85, B:L.88 Hydrogen bonds: A:S.130, A:S.130 TDS.15: 15 residues within 4Å: Chain I: S.130, V.133, T.134, V.151, V.154, L.169, R.182, Y.183, A.186, V.190, L.191 Chain J: P.77, L.81, L.88 Ligands: CLA.17 10 PLIP interactions: 4 interactions with chain J, 6 interactions with chain I Hydrophobic interactions: J:P.77, J:L.81, J:L.81, J:L.88, I:V.133, I:V.151, I:V.154, I:V.154, I:L.169, I:Y.183

2 x PL9: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE(Non-covalent)

PL9.5: 6 residues within 4Å: Chain A: Y.25, F.203 Chain D: T.28 Ligands: HEM.3, OPC.6, OPC.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.25, A:F.203, D:T.28 PL9.19: 9 residues within 4Å: Chain I: L.45 Chain J: L.37, Y.38 Chain L: F.24, T.28, A.34, L.38 Ligands: HEM.14, OPC.20 4 PLIP interactions: 1 interactions with chain I, 2 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: I:L.45, L:F.24, L:L.38, J:L.37

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.6: 6 residues within 4Å: Chain A: K.24 Chain B: N.34, Y.38 Chain D: Q.17 Ligands: PL9.5, OPC.9 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Salt bridges: C:K.276 Hydrogen bonds: B:N.34, D:Q.17 OPC.9: 13 residues within 4Å: Chain A: F.48, F.52, A.196, L.200 Chain D: L.35, L.38, V.39, F.42 Chain I: V.197, L.201, M.205 Ligands: PL9.5, OPC.6 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: I:V.197, I:L.201, A:F.48, A:L.200 OPC.16: 9 residues within 4Å: Chain A: L.168 Chain I: F.48, F.52, F.56, L.200, F.203 Chain L: V.39, F.42 Ligands: TDS.4 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:F.48, I:L.200, I:F.203 OPC.20: 7 residues within 4Å: Chain I: K.24 Chain J: D.35, Y.38 Chain K: K.276 Chain L: Q.17, F.24 Ligands: PL9.19 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:Q.17, L:Q.17 Salt bridges: K:K.275, K:K.276

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.7: 21 residues within 4Å: Chain A: V.101, Y.105, A.125, 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.132, F.133, G.136, T.140, L.143 Ligands: TDS.4 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:L.81, B:V.84, B:I.87, B:A.102, B:V.104, B:P.105, B:L.106, B:L.106, B:L.108, B:I.132, B:F.133, B:F.133, B:F.133, B:L.143, A:Y.105, A:Y.105 Hydrogen bonds: B:V.84 CLA.17: 20 residues within 4Å: Chain I: M.97, I.98, V.101, F.102, A.125, V.126, V.129 Chain J: Y.80, P.83, V.84, I.87, L.100, V.104, P.105, L.106, I.132, F.133, G.136, T.140 Ligands: TDS.15 16 PLIP interactions: 12 interactions with chain J, 4 interactions with chain I, Hydrophobic interactions: J:P.83, J:V.84, J:I.87, J:L.100, J:V.104, J:V.104, J:P.105, J:P.105, J:L.106, J:L.106, J:I.132, J:F.133, I:V.101, I:F.102, I:V.126, I:V.129

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

FES.10: 9 residues within 4Å: Chain D: C.108, H.110, L.111, G.112, C.113, C.126, H.129, G.130, S.131 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.108, D:H.110, D:C.126, D:H.129 FES.21: 10 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 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.11: 21 residues within 4Å: Chain A: F.33, I.39, M.96, L.99 Chain B: V.43, G.46, T.47 Chain E: V.10, A.13, L.14, F.16, G.17, V.20, F.24 Chain F: I.16, F.17, W.20 Chain G: F.22, A.24, A.25, Q.28 14 PLIP interactions: 3 interactions with chain A, 5 interactions with chain E, 4 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: A:F.33, A:I.39, A:L.99, E:V.10, E:L.14, E:F.16, E:V.20, E:F.24, F:I.16, F:I.16, F:F.17, F:F.17, G:F.22, G:A.24 BCR.22: 19 residues within 4Å: Chain I: F.33, I.39, M.96, L.99 Chain J: G.46 Chain M: V.10, A.13, L.14, F.16, G.17, V.20, F.24 Chain N: I.16, F.17, W.20 Chain O: F.22, A.24, A.25, Q.28 16 PLIP interactions: 4 interactions with chain I, 5 interactions with chain N, 5 interactions with chain M, 2 interactions with chain O Hydrophobic interactions: I:F.33, I:F.33, I:I.39, I:L.99, N:I.16, N:I.16, N:F.17, N:F.17, N:W.20, M:V.10, M:L.14, M:F.16, M:V.20, M:F.24, O:F.22, O:A.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kurisu, G. et al., Structure of the Cytochrome B6F Complex of Oxygenic Photosynthesis: Tuning the Cavity. Science (2003)

Release Date

2004-04-20

Peptides

CYTOCHROME B6: AI
SUBUNIT IV: BJ
CYTOCHROME F: CK
RIESKE IRON-SULFUR PROTEIN: DL
PROTEIN PET L: EM
PROTEIN PET M: FN
PROTEIN PET G: GO
PROTEIN PET N: 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

SUBUNIT IV

CYTOCHROME F

RIESKE IRON-SULFUR PROTEIN

PROTEIN PET L

PROTEIN PET M

PROTEIN PET G

PROTEIN PET N

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