SMTL ID : 4pv1.1

Cytochrome B6F structure from M. laminosus with the quinone analog inhibitor stigmatellin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

2 x MYS: PENTADECANE(Non-covalent)

MYS.1: 4 residues within 4Å: Chain A: S.130, T.134, L.169, A.186 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.134, A:L.169 MYS.21: 4 residues within 4Å: Chain I: S.130, T.134, L.169, A.186 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:T.134, I:L.169

4 x CD: CADMIUM ION(Non-covalent)

CD.2: 3 residues within 4Å: Chain A: E.75 Chain C: K.140, H.143 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.143, A:E.75, A:E.75, H2O.1 CD.11: 3 residues within 4Å: Chain B: D.58 Chain C: K.146 Chain G: E.3 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain B Metal complexes: G:E.3, B:D.58, B:D.58 CD.22: 3 residues within 4Å: Chain I: E.75 Chain K: K.140, H.143 4 PLIP interactions: 2 interactions with chain I, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: I:E.75, I:E.75, K:H.143, H2O.2 CD.31: 3 residues within 4Å: Chain J: D.58 Chain K: K.146 Chain O: E.3 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain O Metal complexes: J:D.58, J:D.58, O:E.3

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

HEC.3: 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, T.128, F.131, G.135, L.138, P.139, Y.184, H.187, T.188, P.192 Chain I: F.189 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain I, Hydrophobic interactions: A:F.44, A:F.44, A:Q.47, A:F.48, A:M.54, A:Y.58, A:R.87, A:T.128, A:F.131, A:F.131, A:F.131, A:F.131, A:L.138, A:Y.184, A:P.192, I:F.189 Salt bridges: A:R.83, A:R.83, A:R.87 Metal complexes: A:H.86, A:H.187 HEC.4: 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, T.117, W.118, G.121, V.122, A.125, T.128, M.199, H.202, F.203, I.206, G.210, I.211, S.212 Ligands: HEC.5 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:T.40, A:L.41, A:V.101, A:V.104, A:T.117, A:W.118, A:W.118, A:W.118, A:V.122, A:A.125, A:F.203 Hydrogen bonds: A:G.37, A:G.38, A:S.212 Water bridges: A:Y.34, A:L.36, A:R.114 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 Metal complexes: A:H.100, A:H.202 HEC.5: 20 residues within 4Å: Chain A: V.30, N.31, Y.34, C.35, G.38, L.41, T.42, F.203, I.206, R.207, G.210, I.211 Chain B: N.25, V.39, F.40, V.43, I.44 Chain H: R.26 Ligands: HEC.4, SMA.8 14 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.34, A:F.203, A:I.206, B:V.39, B:F.40, B:F.40, B:F.40, B:V.43, B:I.44, B:I.44 Hydrogen bonds: A:I.211, B:N.25 Salt bridges: A:R.207 Metal complexes: H2O.1 HEC.15: 20 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, P.118, N.154, G.156, R.157, G.158, I.160, Y.161 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.1, C:P.2, C:W.4, C:W.4, C:A.5, C:N.71, C:P.118, C:N.154, C:R.157, C:Y.161, C:Y.161 Hydrogen bonds: C:Q.60, C:N.71, C:N.71 Salt bridges: C:R.157 pi-Stacking: C:Y.1, C:W.4 Metal complexes: C:H.26 HEC.23: 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, T.128, F.131, G.135, L.138, P.139, Y.184, H.187, T.188, P.192 21 PLIP interactions: 20 interactions with chain I, 1 interactions with chain A, Hydrophobic interactions: I:F.44, I:F.44, I:Q.47, I:F.48, I:M.54, I:Y.58, I:R.87, I:T.128, I:F.131, I:F.131, I:F.131, I:F.131, I:L.138, I:Y.184, I:P.192, A:F.189 Salt bridges: I:R.83, I:R.83, I:R.87 Metal complexes: I:H.86, I:H.187 HEC.24: 27 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, R.114, T.117, W.118, G.121, V.122, A.125, T.128, M.199, H.202, F.203, I.206, G.210, I.211, S.212 Ligands: HEC.25 23 PLIP interactions: 23 interactions with chain I, Hydrophobic interactions: I:T.40, I:L.41, I:V.101, I:V.104, I:T.117, I:W.118, I:W.118, I:W.118, I:V.122, I:A.125, I:F.203 Hydrogen bonds: I:G.37, I:G.38, I:S.212 Water bridges: I:Y.34, I:L.36, I:R.114 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 Metal complexes: I:H.100, I:H.202 HEC.25: 20 residues within 4Å: Chain I: V.30, N.31, Y.34, C.35, G.38, L.41, T.42, F.203, I.206, R.207, G.210, I.211 Chain J: N.25, V.39, F.40, V.43, I.44 Chain P: R.26 Ligands: HEC.24, SMA.28 14 PLIP interactions: 5 interactions with chain I, 8 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: I:Y.34, I:F.203, I:I.206, J:V.39, J:F.40, J:F.40, J:F.40, J:V.43, J:I.44, J:I.44 Hydrogen bonds: I:I.211, J:N.25 Salt bridges: I:R.207 Metal complexes: H2O.1 HEC.35: 20 residues within 4Å: Chain K: Y.1, P.2, W.4, A.5, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, P.118, N.154, G.156, R.157, G.158, I.160, Y.161 19 PLIP interactions: 19 interactions with chain K, Hydrophobic interactions: K:Y.1, K:P.2, K:W.4, K:W.4, K:A.5, K:N.71, K:P.118, K:N.154, K:R.157, K:Y.161, K:Y.161 Hydrogen bonds: K:Q.60, K:N.71, K:N.71, K:Y.161 Salt bridges: K:R.157 pi-Stacking: K:Y.1, K:W.4 Metal complexes: K:H.26

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

UMQ.6: 8 residues within 4Å: Chain A: S.120, L.204, M.205, K.208 Chain I: L.12, L.17 Ligands: UMQ.26, UMQ.27 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: I:L.12 Hydrogen bonds: I:L.12, A:K.208 Salt bridges: A:K.208 UMQ.7: 9 residues within 4Å: Chain A: N.3, Y.5, D.6, I.14, Q.15, A.18 Ligands: UMQ.12, OPC.18, UMQ.26 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.14 Hydrogen bonds: A:N.3, A:D.6, A:Q.15, A:Q.15 UMQ.12: 7 residues within 4Å: Chain A: Q.15, A.18, T.22 Chain B: W.32 Ligands: UMQ.7, SMA.8, SQD.17 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.32, B:W.32 Hydrogen bonds: A:Q.15 UMQ.26: 8 residues within 4Å: Chain A: L.12, L.17 Chain I: S.120, L.204, M.205, K.208 Ligands: UMQ.6, UMQ.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: A:L.12 Hydrogen bonds: A:L.12, I:K.208 Salt bridges: I:K.208 UMQ.27: 9 residues within 4Å: Chain I: N.3, Y.5, D.6, I.14, Q.15, A.18 Ligands: UMQ.6, UMQ.32, OPC.38 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:I.14 Hydrogen bonds: I:N.3, I:D.6, I:Q.15, I:Q.15 UMQ.32: 7 residues within 4Å: Chain I: Q.15, A.18, T.22 Chain J: W.32 Ligands: UMQ.27, SMA.28, SQD.37 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:W.32, J:W.32 Hydrogen bonds: I:Q.15

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.8: 9 residues within 4Å: Chain A: K.24, R.207 Chain B: L.36, L.37, F.40 Ligands: HEC.5, 8K6.10, UMQ.12, SQD.17 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.36, B:L.37 Hydrogen bonds: A:R.207, A:R.207 SMA.28: 9 residues within 4Å: Chain I: K.24, R.207 Chain J: L.36, L.37, F.40 Ligands: HEC.25, 8K6.30, UMQ.32, SQD.37 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:L.36, J:L.37 Hydrogen bonds: I:R.207, I:R.207

2 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)

7PH.9: 15 residues within 4Å: Chain A: F.78, L.81 Chain B: F.48, V.52 Chain C: D.251, N.253, R.254, W.257, M.258, F.261 Chain D: G.33, A.34, Y.36, P.37 Ligands: 8K6.10 16 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A, 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: D:A.34, D:Y.36, D:P.37, A:F.78, A:F.78, A:L.81, C:R.254, C:W.257, C:W.257, C:W.257, C:F.261, C:F.261, B:F.48, B:V.52 Hydrogen bonds: D:Y.36 Salt bridges: D:K.40 7PH.29: 15 residues within 4Å: Chain I: F.78, L.81 Chain J: F.48, V.52 Chain K: D.251, N.253, R.254, W.257, M.258, F.261 Chain L: G.33, A.34, Y.36, P.37 Ligands: 8K6.30 15 PLIP interactions: 4 interactions with chain L, 3 interactions with chain I, 2 interactions with chain J, 6 interactions with chain K Hydrophobic interactions: L:A.34, L:Y.36, L:P.37, I:F.78, I:F.78, I:L.81, J:F.48, J:V.52, K:R.254, K:W.257, K:W.257, K:W.257, K:F.261, K:F.261 Salt bridges: L:K.40

2 x 8K6: Octadecane(Non-covalent)

8K6.10: 9 residues within 4Å: Chain A: A.49, I.82, I.85 Chain B: I.44, F.48 Chain D: A.31, A.34 Ligands: SMA.8, 7PH.9 9 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:A.49, A:I.82, A:I.85, B:I.44, B:F.48, B:F.48, B:F.48, B:F.48, D:A.31 8K6.30: 9 residues within 4Å: Chain I: A.49, I.82, I.85 Chain J: I.44, F.48 Chain L: A.31, A.34 Ligands: SMA.28, 7PH.29 9 PLIP interactions: 3 interactions with chain I, 5 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: I:A.49, I:I.82, I:I.85, J:I.44, J:F.48, J:F.48, J:F.48, J:F.48, L:A.31

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.13: 22 residues within 4Å: Chain A: I.98, V.101, F.102, Y.105, A.125, V.129 Chain B: Y.80, P.83, V.84, I.87, M.101, V.104, P.105, L.106, L.108, I.109, I.132, F.133, G.136, V.139, T.140 Ligands: OPC.14 17 PLIP interactions: 5 interactions with chain A, 11 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.106, B:L.108, B:I.109, B:I.132, B:F.133, B:F.133, B:V.139 Metal complexes: H2O.1 CLA.33: 22 residues within 4Å: Chain I: I.98, V.101, F.102, Y.105, A.125, V.129 Chain J: Y.80, P.83, V.84, I.87, M.101, V.104, P.105, L.106, L.108, I.109, I.132, F.133, G.136, V.139, T.140 Ligands: OPC.34 17 PLIP interactions: 11 interactions with chain J, 5 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:V.84, J:I.87, J:V.104, J:V.104, J:L.106, J:L.108, J:I.109, J:I.132, J:F.133, J:F.133, J:V.139, I:V.101, I:F.102, I:Y.105, I:Y.105, I:V.129 Metal complexes: H2O.1

6 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.14: 18 residues within 4Å: Chain A: Y.105 Chain B: I.87, L.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, N.118, R.125, R.126, P.127, V.128, A.129, I.132 Ligands: CLA.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.87, B:L.100, B:L.108, B:V.111, B:I.114, B:I.132 Hydrogen bonds: B:N.118, B:V.128, B:A.129 OPC.18: 7 residues within 4Å: Chain A: F.48, F.52 Chain D: L.38, V.39 Chain I: W.193, V.197 Ligands: UMQ.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: A:F.48, I:W.193, I:V.197 OPC.19: 24 residues within 4Å: Chain A: M.92, M.96 Chain B: T.47, C.50, I.51 Chain C: P.37, Q.38 Chain E: G.4, A.5, Y.8 Chain F: Y.7, A.8, L.11, S.12, G.14, L.15 Chain G: L.5, L.9 Chain H: V.5, W.8, L.11, L.12, F.15 Ligands: BCR.20 16 PLIP interactions: 3 interactions with chain E, 3 interactions with chain H, 2 interactions with chain G, 4 interactions with chain F, 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: E:A.5, E:Y.8, E:Y.8, H:L.11, H:F.15, H:F.15, G:L.5, G:L.9, F:L.11, F:L.11, F:L.11, F:L.15, B:T.47, B:I.51, A:M.92 Hydrogen bonds: C:Q.38 OPC.34: 18 residues within 4Å: Chain I: Y.105 Chain J: I.87, L.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, N.118, R.125, R.126, P.127, V.128, A.129, I.132 Ligands: CLA.33 11 PLIP interactions: 10 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:I.87, J:L.100, J:L.108, J:V.111, J:I.114, J:I.132 Hydrogen bonds: J:E.115, J:N.118, J:V.128, J:A.129, I:Y.105 OPC.38: 7 residues within 4Å: Chain A: W.193, V.197 Chain I: F.48, F.52 Chain L: L.38, V.39 Ligands: UMQ.27 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:W.193, A:V.197, I:F.48 OPC.39: 24 residues within 4Å: Chain I: M.92, M.96 Chain J: T.47, C.50, I.51 Chain K: P.37, Q.38 Chain M: G.4, A.5, Y.8 Chain N: Y.7, A.8, L.11, S.12, G.14, L.15 Chain O: L.5, L.9 Chain P: V.5, W.8, L.11, L.12, F.15 Ligands: BCR.40 15 PLIP interactions: 2 interactions with chain O, 3 interactions with chain M, 1 interactions with chain I, 2 interactions with chain J, 3 interactions with chain N, 3 interactions with chain P, 1 interactions with chain K Hydrophobic interactions: O:L.5, O:L.9, M:A.5, M:Y.8, M:Y.8, I:M.92, J:T.47, J:I.51, N:L.11, N:L.11, N:L.11, P:L.11, P:F.15, P:F.15 Hydrogen bonds: K:Q.38

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

FES.16: 7 residues within 4Å: Chain D: C.108, H.110, L.111, C.113, C.126, H.129, 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.36: 7 residues within 4Å: Chain L: C.108, H.110, L.111, C.113, C.126, H.129, 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.17: 11 residues within 4Å: Chain B: W.32, P.33, Y.38 Chain C: K.275 Chain D: R.16, N.20, L.21, F.24, G.25 Ligands: SMA.8, UMQ.12 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D, 1 interactions with chain B Salt bridges: C:K.275 Hydrophobic interactions: D:L.21, D:F.24, D:F.24 Hydrogen bonds: D:N.20, B:W.32 SQD.37: 11 residues within 4Å: Chain J: W.32, P.33, Y.38 Chain K: K.275 Chain L: R.16, N.20, L.21, F.24, G.25 Ligands: SMA.28, UMQ.32 6 PLIP interactions: 4 interactions with chain L, 1 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: L:L.21, L:F.24, L:F.24 Hydrogen bonds: L:N.20, J:W.32 Salt bridges: K:K.275

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

BCR.20: 16 residues within 4Å: Chain A: I.32, F.33, I.39, M.96 Chain B: V.43, T.47 Chain F: I.16, F.17, W.20 Chain G: L.13, A.16, G.19, G.20, Y.23 Chain H: I.19 Ligands: OPC.19 14 PLIP interactions: 5 interactions with chain A, 2 interactions with chain G, 5 interactions with chain F, 1 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: A:I.32, A:I.32, A:F.33, A:F.33, A:I.39, G:L.13, G:Y.23, F:I.16, F:I.16, F:F.17, F:F.17, F:W.20, H:I.19, B:V.43 BCR.40: 16 residues within 4Å: Chain I: I.32, F.33, I.39, M.96 Chain J: V.43, T.47 Chain N: I.16, F.17, W.20 Chain O: L.13, A.16, G.19, G.20, Y.23 Chain P: I.19 Ligands: OPC.39 14 PLIP interactions: 2 interactions with chain O, 5 interactions with chain I, 1 interactions with chain P, 5 interactions with chain N, 1 interactions with chain J Hydrophobic interactions: O:L.13, O:Y.23, I:I.32, I:I.32, I:F.33, I:F.33, I:I.39, P:I.19, N:I.16, N:I.16, N:F.17, N:F.17, N:W.20, J:V.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasan, S.S. et al., Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal. Biophys.J. (2014)

Release Date

2014-08-20

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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