SMTL ID : 7jro.1

Plant Mitochondrial complex IV from Vigna radiata

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-mer

Ligands

2 x HEA: HEME-A(Non-covalent)

HEA.1: 26 residues within 4Å: Chain A: W.129, W.239, V.246, Y.247, H.292, H.293, T.311, A.315, G.319, I.322, F.350, G.354, I.358, L.360, A.361, D.366, H.370, V.375, H.378, F.379, V.382, L.383, R.440 Chain B: I.46, I.89, L.90 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.129, A:W.239, A:V.246, A:V.246, A:A.315, A:I.322, A:F.350, A:I.358, A:A.361, A:F.379, A:F.379, A:V.382, A:L.383, B:I.46, B:I.89, B:L.90 Hydrogen bonds: A:Y.247, A:Y.247, A:D.366, A:R.440 Salt bridges: A:H.370, A:R.440 pi-Stacking: A:H.293 pi-Cation interactions: A:H.243, A:H.243, A:H.293 Metal complexes: A:H.378 HEA.2: 30 residues within 4Å: Chain A: G.24, A.25, G.28, V.29, T.32, S.35, I.38, R.39, Y.57, I.61, H.64, A.65, M.68, I.69, G.128, W.129, Y.373, F.379, H.380, L.383, S.384, L.391, F.392, V.423, F.427, R.440, R.441, S.460, I.467, F.470 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:I.61, A:A.65, A:M.68, A:F.379, A:F.379, A:L.383, A:L.391, A:F.392, A:F.392, A:F.427, A:I.467, A:F.470, A:F.470 Hydrogen bonds: A:W.129, A:S.384, A:R.441 Salt bridges: A:R.440, A:R.441 pi-Stacking: A:H.64, A:F.379, A:H.380, A:H.380, A:F.427 Metal complexes: A:H.64, A:H.380

1 x CU: COPPER (II) ION(Non-covalent)

CU.3: 3 residues within 4Å: Chain A: H.243, H.292, H.293 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.243, A:H.292, A:H.293

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: H.370, D.371 Chain B: D.196, E.221 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.370, A:D.371, B:E.221

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.5: 11 residues within 4Å: Chain A: M.1, F.9 Chain C: P.16, I.19, L.23 Chain I: K.34, S.37, V.38, L.42 Ligands: PC1.25, 3PE.27 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: I:L.42, A:F.9, C:I.19, C:L.23 PC1.25: 14 residues within 4Å: Chain A: W.106, P.110, L.112, L.113, L.120 Chain C: S.22 Chain I: G.53, Y.57, S.60, H.61 Chain J: Y.84, F.88 Ligands: PC1.5, 3PE.27 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: A:W.106, A:P.110, A:L.112, A:L.113, A:L.113 Hydrogen bonds: I:S.60, I:S.60

17 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.6: 9 residues within 4Å: Chain A: F.172, T.180, M.181, H.182, L.192, L.200, V.284, F.287 Ligands: 3PE.12 Ligand excluded by PLIP 3PE.7: 11 residues within 4Å: Chain A: H.236, F.240, W.290, L.299, D.300, T.303, Y.306 Chain C: M.95, F.98, W.102 Ligands: 3PE.20 Ligand excluded by PLIP 3PE.9: 9 residues within 4Å: Chain A: Y.336, L.341, V.344, F.348, Q.413, W.417 Chain D: M.1, T.3 Ligands: 3PE.16 Ligand excluded by PLIP 3PE.10: 7 residues within 4Å: Chain A: L.411, C.469, V.472, T.475 Chain D: I.16 Chain J: V.71, F.72 Ligand excluded by PLIP 3PE.11: 7 residues within 4Å: Chain A: F.218 Chain C: G.32, Y.35, M.36, S.47 Chain F: L.93 Ligands: 3PE.18 Ligand excluded by PLIP 3PE.12: 8 residues within 4Å: Chain A: F.172, M.181, F.196 Chain C: Y.84, L.88, V.94 Ligands: 3PE.6, 3PE.21 Ligand excluded by PLIP 3PE.14: 4 residues within 4Å: Chain A: W.452, L.455 Chain B: L.19 Ligands: 3PE.24 Ligand excluded by PLIP 3PE.15: 4 residues within 4Å: Chain A: A.327 Chain B: V.53, I.78 Chain H: V.17 Ligand excluded by PLIP 3PE.16: 7 residues within 4Å: Chain A: Y.336 Chain B: L.51, S.55, L.58, R.62, S.63 Ligands: 3PE.9 Ligand excluded by PLIP 3PE.17: 15 residues within 4Å: Chain A: F.97, P.98, R.99, L.100, I.103, L.155, V.158, L.162 Chain C: H.10, V.12, A.25, W.60, W.61, H.74, F.89 Ligand excluded by PLIP 3PE.18: 13 residues within 4Å: Chain A: H.154, F.218 Chain C: Y.184, A.187, T.190, I.191, F.201, G.205, F.206, F.209 Chain F: L.93, F.94 Ligands: 3PE.11 Ligand excluded by PLIP 3PE.19: 14 residues within 4Å: Chain C: M.57, W.61, L.65, T.69, H.74, F.86, F.89, I.213, F.217, R.224, H.229, H.234, V.236, G.237 Ligand excluded by PLIP 3PE.20: 9 residues within 4Å: Chain A: D.230 Chain C: F.98, W.102, F.105, H.106, A.110, T.112, F.254 Ligands: 3PE.7 Ligand excluded by PLIP 3PE.21: 4 residues within 4Å: Chain C: R.83, I.87, V.250 Ligands: 3PE.12 Ligand excluded by PLIP 3PE.22: 6 residues within 4Å: Chain A: L.37 Chain D: I.29, F.30, G.31 Chain J: V.79, V.86 Ligand excluded by PLIP 3PE.24: 14 residues within 4Å: Chain A: T.356, F.432, L.435 Chain B: L.19, G.20, F.21, H.36, H.37, F.40 Chain H: A.30, W.34, H.37, E.41 Ligands: 3PE.14 Ligand excluded by PLIP 3PE.27: 6 residues within 4Å: Chain I: Y.50, R.54, Y.57 Ligands: PC1.5, CDL.8, PC1.25 Ligand excluded by PLIP

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.8: 14 residues within 4Å: Chain A: R.6, W.7, L.8, L.19, I.22, F.403, V.474 Chain J: Y.55, M.60, K.66, M.67, A.70, V.71 Ligands: 3PE.27 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain J Hydrophobic interactions: A:L.8, A:L.19, A:I.22, A:I.22, A:F.403, A:V.474, J:A.70, J:V.71 Hydrogen bonds: A:R.6, J:Y.55 Salt bridges: J:K.66

1 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.13: 6 residues within 4Å: Chain B: H.184, C.219, E.221, C.223, H.227, M.230 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.184, B:C.219, B:C.219, B:E.221, B:C.223, B:C.223, B:H.227

1 x ZN: ZINC ION(Non-covalent)

ZN.23: 5 residues within 4Å: Chain E: C.101, G.103, H.110, C.125, C.128 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.101, E:H.110, E:C.125, E:C.128

1 x LYS: LYSINE(Non-covalent)

LYS.26: 1 residues within 4Å: Chain I: K.65 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:K.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maldonado, M. et al., Atomic structures of respiratory complex III 2 , complex IV, and supercomplex III 2 -IV from vascular plants. Elife (2021)

Release Date

2021-01-20

Peptides

COX1: A
Cytochrome c oxidase subunit 2: B
COX3: C
COX4: D
cytochrome c oxidase subunit 5b-2, mitochondrial: E
cytochrome c oxidase subunit 6a, mitochondrial: F
cytochrome c oxidase subunit 6b-1: G
Cytochrome c oxidase subunit 5C: H
COX7a: I
COX7c: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

C
c

D
d

E
e

F
f

G
g

H
h

I
i

J
j

Membrane

We predict this structure to be a membrane protein.
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COX1

Cytochrome c oxidase subunit 2

COX3

COX4

cytochrome c oxidase subunit 5b-2, mitochondrial

cytochrome c oxidase subunit 6a, mitochondrial

cytochrome c oxidase subunit 6b-1

Cytochrome c oxidase subunit 5C

COX7a

COX7c

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