- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 11 x CDL: CARDIOLIPIN
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE
HEM.3: 19 residues within 4Å:- Chain C: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, A.83, A.86, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, Y.274
12 PLIP interactions:12 interactions with chain C,- Hydrophobic interactions: C:L.40, C:Q.43, C:I.48, C:A.86, C:T.127, C:V.135, C:F.180, C:Y.184
- Salt bridges: C:R.79, C:R.79
- Metal complexes: C:H.82, C:H.183
HEM.4: 18 residues within 4Å:- Chain C: W.30, G.33, L.36, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, I.120, H.197, L.198, L.201, S.206, S.207
- Ligands: UQ6.8
16 PLIP interactions:16 interactions with chain C,- Hydrophobic interactions: C:L.36, C:L.36, C:L.113, C:W.114, C:W.114, C:I.120, C:L.198, C:L.201
- Hydrogen bonds: C:G.33, C:S.105, C:S.207
- Salt bridges: C:H.96, C:K.99, C:K.99
- Metal complexes: C:H.96, C:H.197
HEM.24: 17 residues within 4Å:- Chain M: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, A.83, A.86, T.127, G.131, Y.132, V.135, H.183, Y.184, P.187, Y.274
11 PLIP interactions:11 interactions with chain M,- Hydrophobic interactions: M:L.40, M:Q.43, M:I.48, M:A.86, M:T.127, M:V.135, M:Y.184
- Salt bridges: M:R.79, M:R.79
- Metal complexes: M:H.82, M:H.183
HEM.25: 17 residues within 4Å:- Chain M: W.30, G.33, L.36, H.96, M.97, K.99, S.105, L.113, W.114, G.117, I.120, V.194, H.197, L.201, S.206, S.207
- Ligands: UQ6.30
15 PLIP interactions:15 interactions with chain M,- Hydrophobic interactions: M:L.36, M:L.36, M:L.113, M:W.114, M:W.114, M:I.120, M:L.201
- Hydrogen bonds: M:G.33, M:S.105, M:S.207
- Salt bridges: M:H.96, M:K.99, M:K.99
- Metal complexes: M:H.96, M:H.197
- 26 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
PEF.5: 16 residues within 4Å:- Chain A: S.424
- Chain C: S.34, G.37, L.38, V.41, H.222, S.223, I.226, F.227, D.229, L.230
- Chain D: K.230
- Chain E: S.37
- Ligands: CDL.1, UQ6.8, PCF.19
Ligand excluded by PLIPPEF.6: 10 residues within 4Å:- Chain C: N.7, Y.9, L.10, V.13
- Chain M: T.112, N.115, A.192, M.193, I.195, M.196
Ligand excluded by PLIPPEF.9: 10 residues within 4Å:- Chain C: M.91, T.250, L.251, W.273, L.276, F.333, V.334, G.337, Q.338, A.341
Ligand excluded by PLIPPEF.12: 13 residues within 4Å:- Chain C: I.42, L.81, M.237
- Chain D: L.208, K.211, T.212
- Chain E: G.40, A.41, S.43, T.44, E.46, T.47
- Ligands: PEF.21
Ligand excluded by PLIPPEF.14: 8 residues within 4Å:- Chain C: L.321, F.324
- Chain G: L.34, K.39
- Chain H: K.52, S.53, L.56, Y.57
Ligand excluded by PLIPPEF.17: 9 residues within 4Å:- Chain 5: G.70, S.73, F.74, K.77, G.78
- Chain H: K.34
- Ligands: CDL.13, PCF.18, PEF.41
Ligand excluded by PLIPPEF.20: 8 residues within 4Å:- Chain A: R.327, S.331
- Chain J: R.16, L.17, S.21, L.22, Y.25
- Ligands: CDL.2
Ligand excluded by PLIPPEF.21: 13 residues within 4Å:- Chain C: H.73, N.74
- Chain E: E.46, I.49, S.50, T.53
- Chain J: F.43, T.44, G.46, W.47
- Chain M: D.160, W.164
- Ligands: PEF.12
Ligand excluded by PLIPPEF.27: 11 residues within 4Å:- Chain K: S.424, M.429
- Chain M: S.34, H.222, I.226, F.227, L.230
- Chain N: K.230
- Ligands: CDL.22, UQ6.30, PCF.39
Ligand excluded by PLIPPEF.28: 7 residues within 4Å:- Chain C: T.112, N.115, V.116, M.196, M.199
- Chain M: F.3, N.7
Ligand excluded by PLIPPEF.31: 9 residues within 4Å:- Chain M: M.91, F.94, W.273, L.276, G.337, Q.338, A.341
- Chain R: W.69
- Ligands: PCF.29
Ligand excluded by PLIPPEF.33: 14 residues within 4Å:- Chain M: I.42, N.74, M.237, L.240, A.241
- Chain N: L.208, K.211, T.212
- Chain O: G.40, S.43, T.44, T.47, F.48
- Ligands: PCF.39
Ligand excluded by PLIPPEF.35: 13 residues within 4Å:- Chain C: W.164
- Chain M: H.73
- Chain O: V.45, E.46, I.49, S.50, T.53, A.54
- Chain T: F.43, T.44, G.46, W.47, P.48
Ligand excluded by PLIPPEF.38: 10 residues within 4Å:- Chain M: L.321, F.324, F.325, I.370
- Chain Q: K.39
- Chain R: K.52, S.53, F.55, L.56, Y.57
Ligand excluded by PLIPPEF.40: 8 residues within 4Å:- Chain K: R.327, S.331
- Chain T: R.16, L.17, S.21, L.22, Y.25
- Ligands: CDL.23
Ligand excluded by PLIPPEF.41: 8 residues within 4Å:- Chain 0: F.27
- Chain 5: F.74
- Chain U: K.408, L.409, F.466, Y.470, K.487
- Ligands: PEF.17
Ligand excluded by PLIPPEF.47: 12 residues within 4Å:- Chain U: H.234, F.238, F.285, L.286, W.288, L.297, D.298, T.301, Y.304
- Chain W: L.100, A.103, W.107
Ligand excluded by PLIPPEF.48: 21 residues within 4Å:- Chain U: F.95, P.96, R.97, I.98, I.156, L.159, L.160
- Chain W: H.15, V.17, V.26, S.62, W.65, F.66, I.69, E.72, H.79, G.90, F.91, F.94
- Ligands: PEF.53, PEF.54
Ligand excluded by PLIPPEF.49: 7 residues within 4Å:- Chain U: Y.7
- Chain W: V.25, F.28
- Chain Z: W.19, W.20, Y.33, V.40
Ligand excluded by PLIPPEF.51: 14 residues within 4Å:- Chain 1: K.10, V.13, F.21
- Chain U: F.268, F.321, L.324, A.325
- Chain V: M.42, I.60, H.62, Q.64, I.66, I.69, F.73
Ligand excluded by PLIPPEF.52: 16 residues within 4Å:- Chain 1: F.35
- Chain 4: L.30, P.33, G.34, Y.37
- Chain U: M.350, L.353, T.354, F.426, H.429, F.430
- Chain V: P.5, Y.6, A.7, C.8, L.33
Ligand excluded by PLIPPEF.53: 19 residues within 4Å:- Chain W: L.59, F.66, I.69, V.70, A.73, T.74, I.87, E.98, M.218, M.222, R.229, H.234, L.235, H.239, H.240, V.241, G.242
- Ligands: PEF.48, CDL.55
Ligand excluded by PLIPPEF.54: 21 residues within 4Å:- Chain 3: T.102, L.103, F.104, W.105, N.110
- Chain U: S.204, A.205, T.208, L.212, F.216
- Chain W: Y.189, T.190, A.192, F.194, T.195, I.196, Y.206, A.207, G.210, L.211
- Ligands: PEF.48
Ligand excluded by PLIPPEF.57: 11 residues within 4Å:- Chain 0: P.12, F.13, K.14, R.18, K.19, Y.22, S.25, F.29, F.30
- Chain U: F.19, M.20
Ligand excluded by PLIPPEF.58: 12 residues within 4Å:- Chain 4: S.27, G.31, W.32, A.35, V.36, F.39, S.40, K.41
- Chain U: Y.452, I.456
- Chain V: Y.6
- Ligands: PCF.60
Ligand excluded by PLIPPEF.59: 15 residues within 4Å:- Chain 4: V.25
- Chain 5: L.67, N.68, G.70, D.71, S.72, I.75
- Chain U: L.339, F.346, F.414, W.415, F.418, I.419
- Chain V: S.40, Y.44
Ligand excluded by PLIP- 6 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
PCF.7: 14 residues within 4Å:- Chain C: W.29, F.94, M.95, A.98, Y.102, Y.103, T.317, F.326, F.327, F.333
- Chain G: E.81
- Chain H: Q.54, V.58
- Ligands: CDL.15
14 PLIP interactions:13 interactions with chain C, 1 interactions with chain G- Hydrophobic interactions: C:W.29, C:W.29, C:F.94, C:A.98, C:Y.102, C:Y.102, C:F.326, C:F.333, C:F.333, C:F.333
- Hydrogen bonds: C:Y.102, C:Y.103, C:Y.103
- Salt bridges: G:E.81
PCF.18: 11 residues within 4Å:- Chain 5: G.70, S.73, A.76, K.77
- Chain H: G.38, I.39, F.40, H.41, V.44
- Ligands: CDL.13, PEF.17
7 PLIP interactions:2 interactions with chain 5, 5 interactions with chain H- Hydrophobic interactions: 5:A.76, H:F.40, H:F.40
- Salt bridges: 5:K.77
- Hydrogen bonds: H:G.38, H:F.40, H:H.41
PCF.19: 12 residues within 4Å:- Chain A: D.402, M.429
- Chain E: Y.27, G.34
- Chain I: F.10, K.11, N.13, F.16, V.17, I.20
- Ligands: CDL.1, PEF.5
2 PLIP interactions:1 interactions with chain I, 1 interactions with chain A- Hydrogen bonds: I:N.13
- Salt bridges: A:D.402
PCF.29: 15 residues within 4Å:- Chain M: W.29, F.94, M.95, M.97, A.98, Y.102, Y.103, T.317, F.327, F.333, V.334
- Chain Q: E.81
- Chain R: Q.54
- Ligands: CDL.26, PEF.31
12 PLIP interactions:11 interactions with chain M, 1 interactions with chain Q- Hydrophobic interactions: M:W.29, M:W.29, M:F.94, M:Y.102, M:F.327, M:F.333, M:V.334
- Hydrogen bonds: M:Y.102, M:Y.103, M:Y.103
- Salt bridges: M:K.323, Q:E.81
PCF.39: 12 residues within 4Å:- Chain K: D.402, M.429
- Chain O: Y.27, G.34
- Chain S: F.10, K.11, N.13, V.17, I.20
- Ligands: CDL.22, PEF.27, PEF.33
3 PLIP interactions:2 interactions with chain S, 1 interactions with chain K- Hydrophobic interactions: S:I.20
- Hydrogen bonds: S:N.13
- Salt bridges: K:D.402
PCF.60: 12 residues within 4Å:- Chain 5: F.85, G.88, A.91, V.92, R.94, M.95, G.97, G.98, D.100
- Chain I: W.38
- Chain U: Y.452
- Ligands: PEF.58
7 PLIP interactions:2 interactions with chain U, 5 interactions with chain 5- Hydrogen bonds: U:Y.452, U:Y.452
- Hydrophobic interactions: 5:F.85, 5:A.91, 5:V.92
- Salt bridges: 5:R.94, 5:D.100
- 2 x UQ6: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
UQ6.8: 15 residues within 4Å:- Chain C: Y.16, I.17, S.34, G.37, L.40, I.48, F.49, L.198
- Chain E: M.52
- Chain M: W.164, L.182, L.185
- Ligands: CDL.1, HEM.4, PEF.5
7 PLIP interactions:4 interactions with chain M, 3 interactions with chain C- Hydrophobic interactions: M:W.164, M:L.182, M:L.185, M:L.185, C:L.40, C:I.48, C:F.49
UQ6.30: 15 residues within 4Å:- Chain C: W.164, L.185
- Chain M: I.17, G.33, S.34, V.41, I.48, A.191, V.194, L.198, M.221, D.229
- Chain O: M.52
- Ligands: HEM.25, PEF.27
7 PLIP interactions:5 interactions with chain M, 2 interactions with chain C- Hydrophobic interactions: M:V.41, M:I.48, M:A.191, M:V.194, M:L.198, C:W.164, C:L.185
- 2 x HEC: HEME C
HEC.10: 18 residues within 4Å:- Chain D: V.39, C.40, C.43, H.44, N.108, P.113, L.116, I.119, R.123, Y.129, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.168
15 PLIP interactions:15 interactions with chain D,- Hydrophobic interactions: D:P.113, D:L.116, D:I.119, D:L.133, D:L.134, D:I.162, D:A.163, D:M.164, D:V.167, D:V.167, D:L.168
- Hydrogen bonds: D:Y.129, D:A.163
- Salt bridges: D:R.123
- Metal complexes: D:H.44
HEC.32: 18 residues within 4Å:- Chain N: V.39, C.40, C.43, H.44, N.108, A.111, P.113, P.114, I.119, R.123, Y.129, L.133, L.134, F.157, I.162, A.163, M.164, V.167
13 PLIP interactions:13 interactions with chain N,- Hydrophobic interactions: N:V.39, N:A.111, N:P.113, N:I.119, N:L.133, N:L.134, N:I.162, N:V.167, N:V.167
- Hydrogen bonds: N:Y.129, N:A.163
- Salt bridges: N:R.123
- Metal complexes: N:H.44
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER
FES.11: 9 residues within 4Å:- Chain E: C.129, H.131, L.132, G.133, C.134, C.148, C.150, H.151, S.153
3 PLIP interactions:3 interactions with chain E,- Metal complexes: E:C.129, E:H.131, E:C.148
FES.34: 8 residues within 4Å:- Chain O: C.129, H.131, L.132, G.133, C.134, C.148, H.151, S.153
5 PLIP interactions:5 interactions with chain O,- Metal complexes: O:C.129, O:H.131, O:C.148, O:H.151, O:H.151
- 1 x CU: COPPER (II) ION
- 2 x HEA: HEME-A
HEA.43: 30 residues within 4Å:- Chain U: F.19, I.23, G.26, T.30, S.33, I.36, R.37, F.55, V.59, H.62, A.63, M.66, V.71, G.126, W.127, F.377, H.378, S.382, I.386, L.389, F.390, Y.393, I.417, I.424, F.425, M.428, R.438, R.439, L.465, F.468
26 PLIP interactions:26 interactions with chain U,- Hydrophobic interactions: U:F.19, U:I.23, U:T.30, U:A.63, U:M.66, U:V.71, U:F.377, U:I.386, U:L.389, U:L.389, U:F.390, U:F.390, U:Y.393, U:I.417, U:I.424, U:L.465, U:F.468
- Hydrogen bonds: U:W.127, U:R.439
- Salt bridges: U:R.438, U:R.439
- pi-Stacking: U:F.377, U:H.378, U:F.425
- Metal complexes: U:H.62, U:H.378
HEA.44: 26 residues within 4Å:- Chain U: W.127, W.237, V.244, Y.245, H.290, H.291, T.309, A.313, T.316, G.317, G.352, G.355, V.356, L.358, A.359, D.364, F.367, V.373, H.376, F.377, V.380, L.381, R.438
- Chain V: I.35, P.74, I.77
24 PLIP interactions:21 interactions with chain U, 3 interactions with chain V,- Hydrophobic interactions: U:W.237, U:V.244, U:V.244, U:V.244, U:T.309, U:A.313, U:T.316, U:V.356, U:F.377, U:F.377, U:V.380, U:L.381, U:L.381, U:L.381, V:I.35, V:P.74, V:I.77
- Hydrogen bonds: U:W.127, U:Y.245, U:Y.245
- Salt bridges: U:R.438
- pi-Cation interactions: U:H.241, U:H.376
- Metal complexes: U:H.376
- 1 x CA: CALCIUM ION
- 1 x MG: MAGNESIUM ION
- 1 x CUA: DINUCLEAR COPPER ION
- 1 x ZN: ZINC ION
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lobez, A.P. et al., Electron transfer in the respiratory chain at low salinity. Nat Commun (2024)
- Release Date
- 2024-10-02
- Peptides
- Cytochrome b-c1 complex subunit 1, mitochondrial: AK
Cytochrome b-c1 complex subunit 2, mitochondrial: BL
Cytochrome b: CM
Cytochrome c1, heme protein, mitochondrial: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Cytochrome b-c1 complex subunit 6, mitochondrial: FP
Cytochrome b-c1 complex subunit 7, mitochondrial: GQ
Cytochrome b-c1 complex subunit 8, mitochondrial: HR
Cytochrome b-c1 complex subunit 9, mitochondrial: IS
Cytochrome b-c1 complex subunit 10, mitochondrial: JT
Cytochrome c oxidase subunit 1: U
Cytochrome c oxidase subunit 2: V
Cytochrome c oxidase subunit 3: W
Cytochrome c oxidase subunit 4, mitochondrial: X
Cytochrome c oxidase subunit 6, mitochondrial: Y
Cytochrome c oxidase subunit 7, mitochondrial: Z
Cytochrome c oxidase subunit 8, mitochondrial: 0
Cytochrome c oxidase subunit 9, mitochondrial: 1
Cytochrome c oxidase subunit 12, mitochondrial: 2
Cytochrome c oxidase subunit 13, mitochondrial: 3
Cytochrome c oxidase subunit 26, mitochondrial: 4
Cytochrome c oxidase subunit 5A, mitochondrial: 5 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AK
LB
BL
MC
CM
ND
DN
OE
EO
PF
FP
QG
GQ
RH
HR
SI
IS
TJ
JT
UU
aV
bW
cX
dY
fZ
g0
h1
i2
j3
k4
l5
e - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 11 x CDL: CARDIOLIPIN
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE
- 26 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
- 6 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
- 2 x UQ6: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
- 2 x HEC: HEME C
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER
- 1 x CU: COPPER (II) ION
- 2 x HEA: HEME-A
- 1 x CA: CALCIUM ION
- 1 x MG: MAGNESIUM ION
- 1 x CUA: DINUCLEAR COPPER ION
- 1 x ZN: ZINC ION
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lobez, A.P. et al., Electron transfer in the respiratory chain at low salinity. Nat Commun (2024)
- Release Date
- 2024-10-02
- Peptides
- Cytochrome b-c1 complex subunit 1, mitochondrial: AK
Cytochrome b-c1 complex subunit 2, mitochondrial: BL
Cytochrome b: CM
Cytochrome c1, heme protein, mitochondrial: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Cytochrome b-c1 complex subunit 6, mitochondrial: FP
Cytochrome b-c1 complex subunit 7, mitochondrial: GQ
Cytochrome b-c1 complex subunit 8, mitochondrial: HR
Cytochrome b-c1 complex subunit 9, mitochondrial: IS
Cytochrome b-c1 complex subunit 10, mitochondrial: JT
Cytochrome c oxidase subunit 1: U
Cytochrome c oxidase subunit 2: V
Cytochrome c oxidase subunit 3: W
Cytochrome c oxidase subunit 4, mitochondrial: X
Cytochrome c oxidase subunit 6, mitochondrial: Y
Cytochrome c oxidase subunit 7, mitochondrial: Z
Cytochrome c oxidase subunit 8, mitochondrial: 0
Cytochrome c oxidase subunit 9, mitochondrial: 1
Cytochrome c oxidase subunit 12, mitochondrial: 2
Cytochrome c oxidase subunit 13, mitochondrial: 3
Cytochrome c oxidase subunit 26, mitochondrial: 4
Cytochrome c oxidase subunit 5A, mitochondrial: 5 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AK
LB
BL
MC
CM
ND
DN
OE
EO
PF
FP
QG
GQ
RH
HR
SI
IS
TJ
JT
UU
aV
bW
cX
dY
fZ
g0
h1
i2
j3
k4
l5
e - Membrane
-
We predict this structure to be a membrane protein.