SMTL ID : 2e76.1

Crystal Structure of the Cytochrome b6f Complex with tridecyl-stigmatellin (TDS) from M.laminosus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.41 Å

Oligo State

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

Ligands

2 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: E.75 Chain C: 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.18: 2 residues within 4Å: Chain I: E.75 Chain K: H.143 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: K:H.143, I:E.75, H2O.1

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

HEM.2: 23 residues within 4Å: Chain A: F.44, Q.47, F.48, G.51, F.52, M.54, T.55, Y.58, 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 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:F.48, A:F.52, A:M.54, A:T.55, A:Y.58, A:A.90, A:F.131, A:F.131, A:L.138, I:F.189 Salt bridges: A:R.83, A:R.83, A:R.87 Metal complexes: A:H.86, A:H.187 HEM.3: 25 residues within 4Å: Chain A: Y.34, G.37, G.38, T.40, M.97, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, V.122, L.124, A.125, T.128, H.202, F.203, I.206, G.210, I.211, S.212 Ligands: HEM.4 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:T.40, A:V.101, A:V.104, A:V.104, A:T.117, A:W.118, A:W.118, A:V.122, A:L.124, A:A.125, A:F.203, A:I.206 Hydrogen bonds: A:G.37, A:G.38, A:S.212 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 Metal complexes: A:H.100, A:H.202 HEM.4: 18 residues within 4Å: Chain A: 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, F.40, V.43, I.44 Chain H: R.26 Ligands: HEM.3, TDS.13 10 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.30, A:L.41, A:F.203, A:F.203, B:F.40, B:F.40, B:V.43 Hydrogen bonds: A:I.211 Salt bridges: A:R.207 Metal complexes: H2O.1 HEM.14: 22 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, Y.9, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, V.75, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:Y.1, C:Y.9, C:N.71, C:V.75, C:R.157, C:Y.161, C:Y.161 Hydrogen bonds: C:N.71, C:N.71, C:N.71, C:R.157 Salt bridges: C:R.157 pi-Stacking: C:W.4 Metal complexes: C:H.26 HEM.19: 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, 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 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:F.48, I:F.52, I:M.54, I:T.55, I:Y.58, I:A.90, I:F.131, I:F.131, I:L.138, A:F.189 Salt bridges: I:R.83, I:R.83, I:R.87 Metal complexes: I:H.86, I:H.187 HEM.20: 25 residues within 4Å: Chain I: Y.34, G.37, G.38, T.40, M.97, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, V.122, L.124, A.125, T.128, H.202, F.203, I.206, G.210, I.211, S.212 Ligands: HEM.21 21 PLIP interactions: 21 interactions with chain I, Hydrophobic interactions: I:T.40, I:V.101, I:V.104, I:V.104, I:T.117, I:W.118, I:W.118, I:V.122, I:L.124, I:A.125, I:F.203, I:I.206 Hydrogen bonds: I:G.37, I:G.38, I:S.212 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 Metal complexes: I:H.100, I:H.202 HEM.21: 18 residues within 4Å: Chain I: 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, F.40, V.43, I.44 Chain P: R.26 Ligands: HEM.20, TDS.30 10 PLIP interactions: 6 interactions with chain I, 3 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: I:V.30, I:L.41, I:F.203, I:F.203, J:F.40, J:F.40, J:V.43 Hydrogen bonds: I:I.211 Salt bridges: I:R.207 Metal complexes: H2O.1 HEM.31: 22 residues within 4Å: Chain K: Y.1, P.2, W.4, A.5, Y.9, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, V.75, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 15 PLIP interactions: 15 interactions with chain K, Hydrophobic interactions: K:Y.1, K:Y.9, K:N.71, K:V.75, K:R.157, K:Y.161, K:Y.161 Hydrogen bonds: K:N.71, K:N.71, K:N.71, K:R.157, K:Y.161 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: 19 residues within 4Å: Chain A: M.92 Chain B: C.50 Chain C: P.37, Q.38 Chain E: G.4, A.5, Y.8 Chain F: E.4, Y.7, A.8, L.11, G.14 Chain G: L.5, L.9, L.13 Chain H: W.8, L.12, F.15 Ligands: BCR.17 16 PLIP interactions: 6 interactions with chain H, 4 interactions with chain G, 2 interactions with chain F, 1 interactions with chain C, 1 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: H:W.8, H:W.8, H:L.12, H:F.15, H:F.15, H:F.15, G:L.5, G:L.5, G:L.9, G:L.13, F:A.8, F:L.11, A:M.92, E:Y.8, E:Y.8 Hydrogen bonds: C:Q.38 OPC.11: 13 residues within 4Å: Chain A: Y.105 Chain B: L.100, G.107, V.111, I.114, E.115, V.117, N.118, R.126, P.127, V.128, A.129 Ligands: CLA.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.100, B:V.111 Hydrogen bonds: B:E.115, B:N.118, B:V.128, B:A.129 OPC.22: 19 residues within 4Å: Chain I: M.92 Chain J: C.50 Chain K: P.37, Q.38 Chain M: G.4, A.5, Y.8 Chain N: E.4, Y.7, A.8, L.11, G.14 Chain O: L.5, L.9, L.13 Chain P: W.8, L.12, F.15 Ligands: BCR.34 16 PLIP interactions: 1 interactions with chain I, 6 interactions with chain P, 4 interactions with chain O, 2 interactions with chain N, 1 interactions with chain K, 2 interactions with chain M Hydrophobic interactions: I:M.92, P:W.8, P:W.8, P:L.12, P:F.15, P:F.15, P:F.15, O:L.5, O:L.5, O:L.9, O:L.13, N:A.8, N:L.11, M:Y.8, M:Y.8 Hydrogen bonds: K:Q.38 OPC.28: 13 residues within 4Å: Chain I: Y.105 Chain J: L.100, G.107, V.111, I.114, E.115, V.117, N.118, R.126, P.127, V.128, A.129 Ligands: CLA.27 7 PLIP interactions: 6 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:L.100, J:V.111 Hydrogen bonds: J:E.115, J:N.118, J:V.128, J:A.129, I:Y.105

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

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

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.10: 19 residues within 4Å: Chain A: I.98, V.101, F.102, Y.105 Chain B: Y.80, P.83, V.84, I.87, M.101, V.104, P.105, L.106, L.108, I.132, F.133, G.136, V.139, T.140 Ligands: OPC.11 16 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.87, B:V.104, B:V.104, B:P.105, B:L.106, B:L.108, B:L.108, B:I.132, B:F.133, B:V.139, A:V.101, A:F.102, A:Y.105, A:Y.105 Hydrogen bonds: B:V.84 Metal complexes: H2O.1 CLA.27: 19 residues within 4Å: Chain I: I.98, V.101, F.102, Y.105 Chain J: Y.80, P.83, V.84, I.87, M.101, V.104, P.105, L.106, L.108, I.132, F.133, G.136, V.139, T.140 Ligands: OPC.28 17 PLIP interactions: 4 interactions with chain I, 12 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: I:V.101, I:F.102, I:Y.105, I:Y.105, J:I.87, J:V.104, J:V.104, J:P.105, J:L.106, J:L.108, J:L.108, J:I.132, J:F.133, J:V.139 Hydrogen bonds: J:V.84, J:T.140 Metal complexes: H2O.1

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

TDS.12: 16 residues within 4Å: Chain A: Y.136, V.143, A.147, I.150, V.151, P.155, I.165 Chain B: I.75, L.76, P.77, L.81, F.85, L.88, M.101 Chain L: C.128, H.129 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.150, A:V.151, A:P.155, A:I.165, B:P.77, B:L.81, B:F.85, B:L.88 TDS.13: 9 residues within 4Å: Chain A: V.26, R.207 Chain B: A.31, D.35, L.36, L.37, F.40 Chain D: F.24 Ligands: HEM.4 6 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: D:F.24, B:L.37, B:F.40, B:F.40 Hydrogen bonds: A:R.207, A:R.207 TDS.29: 16 residues within 4Å: Chain D: C.128, H.129 Chain I: Y.136, V.143, A.147, I.150, V.151, P.155, I.165 Chain J: I.75, L.76, P.77, L.81, F.85, L.88, M.101 8 PLIP interactions: 4 interactions with chain J, 4 interactions with chain I Hydrophobic interactions: J:P.77, J:L.81, J:F.85, J:L.88, I:I.150, I:V.151, I:P.155, I:I.165 TDS.30: 9 residues within 4Å: Chain I: V.26, R.207 Chain J: A.31, D.35, L.36, L.37, F.40 Chain L: F.24 Ligands: HEM.21 6 PLIP interactions: 1 interactions with chain L, 3 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: L:F.24, J:L.37, J:F.40, J:F.40 Hydrogen bonds: I:R.207, I:R.207

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.15: 9 residues within 4Å: Chain D: C.108, H.110, L.111, G.112, C.126, C.128, 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.32: 9 residues within 4Å: Chain L: C.108, H.110, L.111, G.112, 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 SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.16: 11 residues within 4Å: Chain B: W.32, P.33, L.37, Y.38 Chain C: K.275, V.279 Chain D: R.16, N.20, L.21, G.25 Ligands: UMQ.9 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: D:L.21 Hydrogen bonds: D:N.20, B:Y.38 Salt bridges: D:R.16, C:K.275 SQD.33: 11 residues within 4Å: Chain J: W.32, P.33, L.37, Y.38 Chain K: K.275, V.279 Chain L: R.16, N.20, L.21, G.25 Ligands: UMQ.26 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: L:L.21 Hydrogen bonds: L:N.20 Salt bridges: L:R.16, K:K.275

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

BCR.17: 15 residues within 4Å: Chain A: F.33, I.39, L.99 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 Ligands: OPC.5 11 PLIP interactions: 3 interactions with chain A, 1 interactions with chain H, 3 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: A:F.33, A:I.39, A:L.99, H:F.15, G:L.13, G:Y.23, G:Y.23, F:I.16, F:I.16, F:F.17, F:F.17 BCR.34: 15 residues within 4Å: Chain I: F.33, I.39, L.99 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 Ligands: OPC.22 11 PLIP interactions: 3 interactions with chain O, 1 interactions with chain P, 3 interactions with chain I, 4 interactions with chain N Hydrophobic interactions: O:L.13, O:Y.23, O:Y.23, P:F.15, I:F.33, I:I.39, I:L.99, N:I.16, N:I.16, N:F.17, N:F.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamashita, E. et al., Structure of the Cytochrome b(6)f Complex: Quinone Analogue Inhibitors as Ligands of Heme c(n). J.Mol.Biol. (2007)

Release Date

2007-06-12

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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