SMTL ID : 1m56.1 (1 other biounit)

Structure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.284, H.333, H.334 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.284, A:H.333, A:H.334 CU.8: 5 residues within 4Å: Chain B: C.227, E.229, C.231, H.235 Ligands: CU.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.227, B:E.229, B:C.231, B:H.235 CU.9: 5 residues within 4Å: Chain B: H.192, C.227, C.231, M.238 Ligands: CU.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.192, B:C.227, B:C.231

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.411, D.412 Chain B: E.229 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.411, A:D.412, B:E.229, H2O.2, H2O.5

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.54, A.57, P.58, G.59, Q.61 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.54, A:E.54, A:A.57, A:G.59, H2O.2

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

HEA.4: 33 residues within 4Å: Chain A: L.34, G.37, G.38, V.45, T.48, M.51, R.52, W.95, I.99, H.102, G.103, M.106, M.107, G.171, W.172, Y.414, F.420, H.421, M.424, S.425, V.429, I.432, F.433, I.436, M.460, T.467, F.468, Q.471, R.481, R.482, A.501, S.504, F.508 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:I.99, A:M.106, A:F.420, A:M.424, A:V.429, A:I.432, A:F.433, A:I.436, A:T.467, A:F.468, A:F.468, A:A.501, A:F.508 Hydrogen bonds: A:T.48, A:T.48, A:R.52, A:W.172, A:Q.471, A:R.482 Water bridges: A:R.481, A:Y.483 Salt bridges: A:R.481, A:R.482 pi-Stacking: A:H.102, A:F.420, A:H.421, A:F.468 Metal complexes: A:H.102, A:H.421 HEA.5: 29 residues within 4Å: Chain A: W.172, W.280, V.287, Y.288, V.291, H.333, H.334, Y.336, T.352, I.355, A.356, T.359, G.360, I.363, F.391, G.395, G.398, L.401, S.402, D.407, H.411, V.416, H.419, F.420, V.423, M.424, R.481 Chain B: I.43, P.83 25 PLIP interactions: 22 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:V.291, A:T.352, A:A.356, A:I.363, A:F.391, A:L.401, A:L.401, A:V.416, A:F.420, A:F.420, A:V.423, B:I.43, B:I.43, B:P.83 Hydrogen bonds: A:W.172, A:Y.288 Water bridges: A:D.412, A:R.481 Salt bridges: A:H.411, A:R.481 pi-Stacking: A:H.419 Metal complexes: A:H.419

6 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.6: 20 residues within 4Å: Chain A: F.135, P.136, R.137, M.138, L.145, A.199, I.202, L.203, L.243, A.247 Chain C: H.10, L.12, M.55, W.58, W.59, H.71, L.79, G.82, F.83, F.86 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:L.145, A:A.199, A:I.202, A:L.203, A:A.247, C:W.58, C:W.59, C:F.83, C:F.86, C:F.86 Hydrogen bonds: A:F.135, A:R.137, A:R.137, A:M.138, C:H.71 Salt bridges: A:R.137 3PE.7: 22 residues within 4Å: Chain A: L.213, R.216, T.221, M.222, W.230, W.237, Y.318, V.321, V.325, F.328, V.329 Chain C: V.91 Chain D: Q.20, K.23, T.24, G.27, F.28, M.31, V.32, A.35 Ligands: 3PE.11, 3PE.13 17 PLIP interactions: 13 interactions with chain A, 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: A:L.213, A:W.237, A:W.237, A:W.237, A:V.321, A:V.321, A:V.325, A:F.328, A:V.329, D:V.32, C:V.91 Hydrogen bonds: A:R.216, A:R.216, A:M.222, D:Q.20 Salt bridges: A:H.223, D:K.23 3PE.10: 21 residues within 4Å: Chain C: L.52, M.55, W.59, V.62, V.63, S.66, L.67, H.71, L.79, F.83, F.86, F.211, F.219, V.222, R.226, H.231, F.232, K.236, H.237, V.238, G.239 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.52, C:W.59, C:W.59, C:W.59, C:F.83, C:F.86, C:F.211, C:F.219, C:V.222, C:V.222 Hydrogen bonds: C:S.66, C:V.238, C:G.239 Salt bridges: C:H.71, C:H.71, C:R.226, C:R.226 3PE.11: 20 residues within 4Å: Chain A: H.277, F.281, W.331, Q.344 Chain B: R.209 Chain C: V.91, W.99, F.102, K.103, Y.107, P.114, F.249, V.252, V.253, F.256 Chain D: A.36, L.43 Ligands: 3PE.7, 3PE.12, 3PE.13 17 PLIP interactions: 5 interactions with chain A, 10 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:F.281, A:W.331, A:W.331, C:V.91, C:F.102, C:F.249, C:V.252, C:V.253, C:F.256, D:L.43 Hydrogen bonds: A:Q.344, C:P.114, B:R.209 Salt bridges: A:H.277, C:K.103 Water bridges: C:K.103, C:D.117 3PE.12: 15 residues within 4Å: Chain C: R.80, I.84, I.87, M.88, H.152, W.245, H.248, V.252 Chain D: F.25, V.29, V.32, T.33, A.36, V.37 Ligands: 3PE.11 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.84, C:I.84, C:I.87, C:W.245, C:W.245, C:H.248, C:V.252, D:V.32, D:T.33, D:A.36, D:V.37 Salt bridges: C:R.80 3PE.13: 17 residues within 4Å: Chain A: L.241, F.281, F.328, V.329, Q.344, Y.347 Chain C: Y.107, L.255, F.256 Chain D: I.39, L.43, L.46, A.47, N.50, A.51 Ligands: 3PE.7, 3PE.11 13 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: A:L.241, A:F.281, A:Y.347, A:Y.347, D:I.39, D:L.43, D:A.47, C:L.255, C:F.256 Hydrogen bonds: A:Q.344, D:N.50, D:A.51, C:Y.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Svensson-Ek, M. et al., The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides. J.Mol.Biol. (2002)

Release Date

2002-08-28

Peptides

CYTOCHROME C OXIDASE: A
CYTOCHROME C OXIDASE: B
CYTOCHROME C OXIDASE: C
CYTOCHROME C OXIDASE: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

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