SMTL ID : 1m57.1 (1 other biounit)

Structure of cytochrome c oxidase from Rhodobacter sphaeroides (EQ(I-286) mutant))

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-oligomer

Ligands

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

CU.1: 5 residues within 4Å: Chain B: C.227, E.229, C.231, H.235 Ligands: CU.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.227, B:E.229, B:C.231, B:H.235 CU.2: 5 residues within 4Å: Chain B: H.192, C.227, C.231, M.238 Ligands: CU.1 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.192, B:C.227, B:C.231 CU.3: 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: H.411, D.412 Chain B: D.204, 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.103, H2O.105

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.46

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

HEA.6: 31 residues within 4Å: Chain A: G.37, G.38, T.48, M.51, R.52, W.95, I.99, T.100, H.102, G.103, M.106, V.110, G.171, W.172, Y.414, F.420, H.421, M.424, S.425, V.429, I.432, I.436, M.460, T.467, F.468, Q.471, R.481, R.482, A.501, S.504, F.508 33 PLIP interactions: 33 interactions with chain A, Hydrophobic interactions: A:T.48, A:I.99, A:I.99, A:M.106, A:V.110, A:Y.414, A:F.420, A:M.424, A:V.429, A:I.432, A:I.436, A:T.467, A:F.468, A:F.468, A:A.501, A:F.508, A:F.508 Hydrogen bonds: A:T.48, A:T.48, A:R.52, A:W.172, A:Q.471, A:R.482, A:Y.483 Water bridges: A:R.482 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.7: 28 residues within 4Å: Chain A: M.107, W.172, W.280, V.287, Y.288, H.333, H.334, T.352, I.355, A.356, T.359, G.360, F.391, G.395, G.398, I.399, 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 23 PLIP interactions: 20 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:T.352, A:F.391, A:F.391, A:I.399, 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, A:D.412 Salt bridges: A:H.411, A:R.481 pi-Stacking: A:H.419 pi-Cation interactions: A:H.284 Metal complexes: A:H.419

6 x PEH: DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEH.8: 21 residues within 4Å: Chain C: L.52, M.55, W.59, V.62, V.63, S.66, L.67, H.71, F.83, F.86, F.211, F.219, V.222, R.226, H.231, F.232, K.236, H.237, V.238, G.239 Ligands: PEH.9 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: 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:S.66, C:H.231, C:V.238, C:G.239 Salt bridges: C:H.71, C:H.71, C:R.226, C:R.226 PEH.9: 20 residues within 4Å: Chain A: F.135, P.136, R.137, M.138, L.141, L.145, I.202, L.203, A.247 Chain C: H.10, M.55, W.58, W.59, H.71, L.79, G.82, F.83, F.86, F.93 Ligands: PEH.8 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:L.141, A:L.145, A:I.202, A:L.203, A:A.247, C:W.58, C:F.83, C:F.86, C:F.86, C:F.93 Hydrogen bonds: A:R.137, A:R.137, A:M.138, C:W.58, C:H.71 Salt bridges: A:R.137 PEH.10: 18 residues within 4Å: Chain A: H.277, F.281, W.331, Q.344 Chain B: R.209 Chain C: V.91, W.99, K.103, Y.107, P.114, V.252, V.253, F.256 Chain D: A.36, L.43 Ligands: PEH.11, PEH.12, PEH.13 15 PLIP interactions: 6 interactions with chain C, 7 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:W.99, C:V.252, C:V.253, C:V.253, C:F.256, A:F.281, A:F.281, A:W.331, A:W.331, D:L.43 Salt bridges: C:K.103, A:H.277 Hydrogen bonds: A:Q.344, A:Q.344, B:R.209 PEH.11: 17 residues within 4Å: Chain A: L.241, V.329, Q.344, Y.347, F.348 Chain C: Y.107, L.255, F.256, A.259 Chain D: I.39, L.43, L.46, A.47, N.50, A.51 Ligands: PEH.10, PEH.12 19 PLIP interactions: 7 interactions with chain A, 5 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: A:L.241, A:Y.347, A:Y.347, A:F.348, C:L.255, C:F.256, C:F.256, C:A.259, D:I.39, D:L.43, D:L.46, D:L.46, D:A.47 Hydrogen bonds: A:Q.344, C:Y.107, D:N.50, D:N.50 Water bridges: A:S.341, A:S.341 PEH.12: 18 residues within 4Å: Chain A: R.216, T.221, M.222, W.230, F.233, W.237, V.321, V.325 Chain C: M.88, V.91 Chain D: Q.20, K.23, T.24, G.27, M.31, A.35 Ligands: PEH.10, PEH.11 14 PLIP interactions: 12 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:W.230, A:F.233, A:W.237, A:W.237, A:W.237, A:W.237, A:V.325, A:V.325, C:V.91 Hydrogen bonds: A:R.216, A:R.216, A:M.222, D:Q.20 Salt bridges: A:H.223 PEH.13: 11 residues within 4Å: Chain C: R.80, I.84, H.152, I.244, W.245, H.248 Chain D: F.25, V.32, A.36, V.37 Ligands: PEH.10 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.84, C:I.84, C:I.244, C:W.245, C:W.245, C:H.248, D:V.32, D:A.36, D:V.37 Salt bridges: C:R.80

Links

RCSB   PDBe   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

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

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