- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.70 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-mer
- Ligands
- 8 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 10 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)
UMQ.4: 10 residues within 4Å:- Chain A: N.3, Y.5, L.12, I.14, I.17, A.18
- Chain I: F.201, M.205
- Ligands: UMQ.5, SQD.16
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:I.14, A:I.14
- Hydrogen bonds: A:N.3
UMQ.5: 11 residues within 4Å:- Chain A: Q.15, I.17, A.18, E.19, V.21, T.22
- Chain B: W.32
- Chain C: N.288
- Ligands: UMQ.4, UMQ.7, SQD.16
9 PLIP interactions:5 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C- Hydrophobic interactions: A:A.18, B:W.32, B:W.32
- Hydrogen bonds: A:Q.15, A:A.18, A:E.19, A:E.19, C:N.288, C:N.288
UMQ.7: 18 residues within 4Å:- Chain A: K.24, V.26, L.41, R.207
- Chain B: A.31, W.32, L.36, L.37, F.40, P.41, I.44
- Chain D: F.24, V.27, T.28, A.31
- Ligands: HEM.3, UMQ.5, SQD.16
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.207, A:R.207
UMQ.9: 15 residues within 4Å:- Chain A: M.1, A.2, N.3, V.4, W.7, F.8, R.11
- Chain I: K.112, L.116, V.119, S.120, I.123, F.198, F.201
- Chain J: F.113
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain I- Hydrophobic interactions: A:W.7
- Hydrogen bonds: A:N.3, A:R.11, I:K.112
UMQ.18: 23 residues within 4Å:- Chain A: I.98, F.102
- Chain B: W.79, Y.80, Y.82, P.83, T.137, T.140, L.141, G.144, I.145, A.148, L.149
- Chain F: M.1, S.2, L.5
- Chain G: V.2, P.4, S.7, V.10, L.11, I.14
- Ligands: CLA.10
7 PLIP interactions:1 interactions with chain F, 5 interactions with chain B, 1 interactions with chain G- Hydrogen bonds: F:S.2, B:I.145
- Hydrophobic interactions: B:W.79, B:Y.82, B:T.140, B:L.141, G:I.14
UMQ.24: 10 residues within 4Å:- Chain A: F.201, M.205
- Chain I: N.3, Y.5, L.12, I.14, I.17, A.18
- Ligands: UMQ.25, SQD.36
3 PLIP interactions:3 interactions with chain I- Hydrophobic interactions: I:I.14, I:I.14
- Hydrogen bonds: I:N.3
UMQ.25: 11 residues within 4Å:- Chain I: Q.15, I.17, A.18, E.19, V.21, T.22
- Chain J: W.32
- Chain K: N.288
- Ligands: UMQ.24, UMQ.27, SQD.36
8 PLIP interactions:4 interactions with chain I, 2 interactions with chain J, 2 interactions with chain K- Hydrophobic interactions: I:A.18, J:W.32, J:W.32
- Hydrogen bonds: I:Q.15, I:A.18, I:E.19, K:N.288, K:N.288
UMQ.27: 18 residues within 4Å:- Chain I: K.24, V.26, L.41, R.207
- Chain J: A.31, W.32, L.36, L.37, F.40, P.41, I.44
- Chain L: F.24, V.27, T.28, A.31
- Ligands: HEM.23, UMQ.25, SQD.36
2 PLIP interactions:2 interactions with chain I- Hydrogen bonds: I:R.207, I:R.207
UMQ.29: 15 residues within 4Å:- Chain A: K.112, L.116, V.119, S.120, I.123, F.198, F.201
- Chain B: F.113
- Chain I: M.1, A.2, N.3, V.4, W.7, F.8, R.11
4 PLIP interactions:1 interactions with chain A, 3 interactions with chain I- Hydrogen bonds: A:K.112, I:N.3, I:R.11
- Hydrophobic interactions: I:W.7
UMQ.38: 23 residues within 4Å:- Chain I: I.98, F.102
- Chain J: W.79, Y.80, Y.82, P.83, T.137, T.140, L.141, G.144, I.145, A.148, L.149
- Chain N: M.1, S.2, L.5
- Chain O: V.2, P.4, S.7, V.10, L.11, I.14
- Ligands: CLA.30
7 PLIP interactions:5 interactions with chain J, 1 interactions with chain N, 1 interactions with chain O- Hydrophobic interactions: J:W.79, J:Y.82, J:T.140, J:L.141, O:I.14
- Hydrogen bonds: J:I.145, N:S.2
- 2 x MYS: PENTADECANE(Non-covalent)
MYS.6: 15 residues within 4Å:- Chain A: V.126, I.127, V.129, S.130, V.133, T.134, L.169, R.182, Y.183, A.186, V.190, L.191, L.194
- Chain I: F.56
- Ligands: CLA.10
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:T.134, A:L.169
MYS.26: 15 residues within 4Å:- Chain A: F.56
- Chain I: V.126, I.127, V.129, S.130, V.133, T.134, L.169, R.182, Y.183, A.186, V.190, L.191, L.194
- Ligands: CLA.30
2 PLIP interactions:2 interactions with chain I- Hydrophobic interactions: I:T.134, I:L.169
- 2 x 8K6: Octadecane(Non-covalent)
8K6.8: 15 residues within 4Å:- Chain A: L.41, F.44, L.45, F.48, A.49, F.52, A.196, M.199, L.200, F.203
- Chain I: F.189, V.190, W.193, L.194, V.197
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain I- Hydrophobic interactions: A:F.48, A:F.52, I:W.193, I:L.194
8K6.28: 15 residues within 4Å:- Chain A: F.189, V.190, W.193, L.194, V.197
- Chain I: L.41, F.44, L.45, F.48, A.49, F.52, A.196, M.199, L.200, F.203
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain I- Hydrophobic interactions: A:W.193, A:L.194, I:F.48, I:F.52
- 2 x CLA: CHLOROPHYLL A(Non-covalent)
CLA.10: 35 residues within 4Å:- Chain A: M.97, I.98, V.101, F.102, Y.105, W.118, V.122, I.123, A.125, V.126, 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.109, V.111, A.129, V.132, F.133, F.135, G.136, V.139, T.140, L.143
- Ligands: MYS.6, OPC.11, UMQ.18
16 PLIP interactions:10 interactions with chain B, 5 interactions with chain A, 1 Ligand-Water interactions,- Hydrophobic interactions: B:L.81, B:V.84, B:I.87, B:V.104, B:L.108, B:F.133, B:F.133, B:V.139, A:I.98, A:F.102, A:Y.105, A:Y.105, A:V.129
- Hydrogen bonds: B:V.84
- pi-Stacking: B:F.133
- Metal complexes: H2O.2
CLA.30: 35 residues within 4Å:- Chain I: M.97, I.98, V.101, F.102, Y.105, W.118, V.122, I.123, A.125, V.126, V.129
- Chain J: Y.80, L.81, P.83, V.84, I.87, M.101, A.102, V.104, P.105, L.106, L.108, I.109, V.111, A.129, V.132, F.133, F.135, G.136, V.139, T.140, L.143
- Ligands: MYS.26, OPC.31, UMQ.38
16 PLIP interactions:5 interactions with chain I, 10 interactions with chain J, 1 Ligand-Water interactions,- Hydrophobic interactions: I:I.98, I:F.102, I:Y.105, I:Y.105, I:V.129, J:L.81, J:V.84, J:I.87, J:V.104, J:L.108, J:F.133, J:F.133, J:V.139
- Hydrogen bonds: J:V.84
- pi-Stacking: J:F.133
- Metal complexes: H2O.6
- 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.11: 22 residues within 4Å:- Chain A: Y.105
- Chain B: I.87, A.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, V.117, N.118, F.120, R.125, R.126, P.127, V.128, A.129, V.132, V.139, L.143
- Ligands: CLA.10
6 PLIP interactions:4 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:I.87
- Hydrogen bonds: B:N.118, B:V.128, B:A.129, A:Y.105
- Water bridges: A:K.111
OPC.13: 37 residues within 4Å:- Chain A: I.39, C.43, M.92, M.96
- Chain B: S.47, C.50, I.51, L.54
- Chain C: P.37, Q.38, S.39, V.40, F.46
- Chain E: A.3, I.4, Y.7, I.8, L.11
- Chain F: E.4, N.7, A.8, L.11, S.12, L.15, V.18, L.22
- Chain G: L.5, I.9, L.13
- Chain H: M.1, L.4, T.5, W.8, L.11, L.12, F.15
- Ligands: BCR.20
17 PLIP interactions:5 interactions with chain H, 4 interactions with chain E, 2 interactions with chain C, 4 interactions with chain F, 1 interactions with chain A, 1 interactions with chain G- Hydrophobic interactions: H:L.12, H:L.12, H:F.15, H:F.15, H:F.15, E:A.3, E:Y.7, E:Y.7, E:I.8, F:A.8, F:L.11, F:L.11, A:I.39, G:L.5
- Hydrogen bonds: C:Q.38, C:S.39, F:E.4
OPC.31: 22 residues within 4Å:- Chain I: Y.105
- Chain J: I.87, A.100, S.103, V.104, G.107, L.108, V.111, I.114, E.115, V.117, N.118, F.120, R.125, R.126, P.127, V.128, A.129, V.132, V.139, L.143
- Ligands: CLA.30
7 PLIP interactions:5 interactions with chain J, 2 interactions with chain I- Hydrophobic interactions: J:I.87
- Hydrogen bonds: J:E.115, J:N.118, J:V.128, J:A.129, I:Y.105
- Water bridges: I:K.111
OPC.33: 37 residues within 4Å:- Chain I: I.39, C.43, M.92, M.96
- Chain J: S.47, C.50, I.51, L.54
- Chain K: P.37, Q.38, S.39, V.40, F.46
- Chain M: A.3, I.4, Y.7, I.8, L.11
- Chain N: E.4, N.7, A.8, L.11, S.12, L.15, V.18, L.22
- Chain O: L.5, I.9, L.13
- Chain P: M.1, L.4, T.5, W.8, L.11, L.12, F.15
- Ligands: BCR.40
16 PLIP interactions:1 interactions with chain I, 2 interactions with chain K, 3 interactions with chain N, 4 interactions with chain M, 5 interactions with chain P, 1 interactions with chain O- Hydrophobic interactions: I:I.39, N:A.8, N:L.11, N:L.11, M:A.3, M:Y.7, M:Y.7, M:I.8, P:L.12, P:L.12, P:F.15, P:F.15, P:F.15, O:L.5
- Hydrogen bonds: K:Q.38, K:S.39
- 2 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)
7PH.14: 18 residues within 4Å:- Chain A: F.78, W.80, L.81
- Chain B: F.48, V.52, V.56
- Chain C: D.251, N.253, R.254, W.257, L.258, A.260, F.261, L.264
- Chain D: G.33, A.34, Y.36, P.37
11 PLIP interactions:5 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A, 3 interactions with chain D- Hydrophobic interactions: C:R.254, C:W.257, C:W.257, C:F.261, B:F.48, B:V.52, A:W.80, D:Y.36, D:Y.36, D:P.37
- Hydrogen bonds: C:D.251
7PH.34: 18 residues within 4Å:- Chain I: F.78, W.80, L.81
- Chain J: F.48, V.52, V.56
- Chain K: D.251, N.253, R.254, W.257, L.258, A.260, F.261, L.264
- Chain L: G.33, A.34, Y.36, P.37
10 PLIP interactions:3 interactions with chain L, 4 interactions with chain K, 1 interactions with chain I, 2 interactions with chain J- Hydrophobic interactions: L:Y.36, L:Y.36, L:P.37, K:R.254, K:W.257, K:W.257, K:F.261, I:W.80, J:F.48, J:V.52
- 2 x CD: CADMIUM ION(Non-covalent)
- 2 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
SQD.16: 12 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, F.24
- Ligands: UMQ.4, UMQ.5, UMQ.7
4 PLIP interactions:2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: D:N.20, B:W.32
- Salt bridges: D:R.16, C:K.275
SQD.36: 12 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, F.24
- Ligands: UMQ.24, UMQ.25, UMQ.27
4 PLIP interactions:1 interactions with chain K, 2 interactions with chain L, 1 interactions with chain J- Salt bridges: K:K.275, L:R.16
- Hydrogen bonds: L:N.20, J:W.32
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.17: 10 residues within 4Å:- Chain D: C.108, H.110, L.111, G.112, C.113, C.126, C.128, 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.37: 10 residues within 4Å:- Chain L: C.108, H.110, L.111, G.112, C.113, C.126, C.128, 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 OCT: N-OCTANE(Non-covalent)
OCT.19: 4 residues within 4Å:- Chain F: F.17, W.20, A.21, A.24
3 PLIP interactions:3 interactions with chain F- Hydrophobic interactions: F:W.20, F:W.20, F:A.24
OCT.39: 4 residues within 4Å:- Chain N: F.17, W.20, A.21, A.24
3 PLIP interactions:3 interactions with chain N- Hydrophobic interactions: N:W.20, N:W.20, N:A.24
- 2 x BCR: BETA-CAROTENE(Non-covalent)
BCR.20: 27 residues within 4Å:- Chain A: I.32, F.33, C.35, L.36, I.39, M.96, L.99
- Chain B: I.42, V.43, G.46, S.47
- Chain F: I.16, F.17, W.20
- Chain G: L.13, V.16, T.17, A.19, G.20, Y.23, Y.26, K.30
- Chain H: F.15, S.18, I.19, V.22
- Ligands: OPC.13
18 PLIP interactions:5 interactions with chain A, 5 interactions with chain F, 2 interactions with chain H, 6 interactions with chain G- Hydrophobic interactions: A:I.32, A:F.33, A:F.33, A:I.39, A:L.99, F:I.16, F:I.16, F:F.17, F:F.17, F:W.20, H:I.19, H:V.22, G:L.13, G:A.19, G:Y.23, G:Y.23, G:Y.23, G:Y.23
BCR.40: 27 residues within 4Å:- Chain I: I.32, F.33, C.35, L.36, I.39, M.96, L.99
- Chain J: I.42, V.43, G.46, S.47
- Chain N: I.16, F.17, W.20
- Chain O: L.13, V.16, T.17, A.19, G.20, Y.23, Y.26, K.30
- Chain P: F.15, S.18, I.19, V.22
- Ligands: OPC.33
18 PLIP interactions:6 interactions with chain O, 5 interactions with chain N, 5 interactions with chain I, 2 interactions with chain P- Hydrophobic interactions: O:L.13, O:A.19, O:Y.23, O:Y.23, O:Y.23, O:Y.23, N:I.16, N:I.16, N:F.17, N:F.17, N:W.20, I:I.32, I:F.33, I:F.33, I:I.39, I:L.99, P:I.19, P:V.22
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hasan, S.S. et al., Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex. Proc.Natl.Acad.Sci.USA (2013)
- Release Date
- 2013-02-20
- Peptides
- Cytochrome b6: AI
Cytochrome b6-f complex subunit 4: BJ
Apocytochrome f: CK
Cytochrome b6-f complex iron-sulfur subunit 1: 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
AI
AB
BJ
BC
CK
CD
DL
DE
EM
EF
FN
FG
GO
GH
HP
H - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.70 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-mer
- Ligands
- 8 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 10 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)
- 2 x MYS: PENTADECANE(Non-covalent)
- 2 x 8K6: Octadecane(Non-covalent)
- 2 x CLA: CHLOROPHYLL A(Non-covalent)
- 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)
- 2 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)
- 2 x CD: CADMIUM ION(Non-covalent)
- 2 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 2 x OCT: N-OCTANE(Non-covalent)
- 2 x BCR: BETA-CAROTENE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hasan, S.S. et al., Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex. Proc.Natl.Acad.Sci.USA (2013)
- Release Date
- 2013-02-20
- Peptides
- Cytochrome b6: AI
Cytochrome b6-f complex subunit 4: BJ
Apocytochrome f: CK
Cytochrome b6-f complex iron-sulfur subunit 1: 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
AI
AB
BJ
BC
CK
CD
DL
DE
EM
EF
FN
FG
GO
GH
HP
H - Membrane
-
We predict this structure to be a membrane protein.