SMTL ID : 1m57.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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: 4 residues within 4Å: Chain A: H.411, D.412 Chain B: D.204, E.229 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.229, A:H.411, A:D.412, H2O.5, H2O.5

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: E.54, A.57, P.58, G.59, V.60, 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:P.58, H2O.2

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

HEA.4: 31 residues within 4Å: Chain A: G.37, G.38, V.45, T.48, M.51, R.52, W.95, I.99, T.100, H.102, G.103, M.106, 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 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:T.48, A:I.99, A:I.99, A:M.106, A:F.420, A:F.420, A:M.424, A:V.429, A:I.432, A:I.436, A:T.467, A:F.468, A:A.501, A:F.508 Hydrogen bonds: A:T.48, A:T.48, A:R.52, A:T.100, A:W.172, A:Y.414, A:Q.471, A:R.482 Water bridges: A:R.481, A:R.481, A:Y.483 Salt bridges: A:R.481, A:R.482 pi-Stacking: A:F.420, A:F.468 Metal complexes: A:H.102, A:H.421 HEA.5: 30 residues within 4Å: Chain A: M.107, W.172, W.280, V.287, Y.288, V.291, 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, L.87 27 PLIP interactions: 3 interactions with chain B, 24 interactions with chain A, Hydrophobic interactions: B:I.43, B:P.83, B:L.87, A:W.280, A:V.287, A:V.287, A:V.291, A:V.291, A:T.352, A:A.356, A:F.391, A:F.391, A:I.399, A:I.399, A:L.401, A:V.416, A:F.420, A:F.420, A:V.423 Hydrogen bonds: A:W.172, A:Y.288 Water bridges: A:R.481, 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: 21 residues within 4Å: Chain A: F.135, P.136, R.137, M.138, L.145, G.198, I.202, L.203, L.243, A.247 Chain C: H.10, M.55, W.58, W.59, E.65, H.71, G.82, F.83, F.86, F.93 Ligands: 3PE.10 16 PLIP interactions: 7 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:W.58, C:W.59, C:F.83, C:F.86, C:F.86, C:F.93, A:L.145, A:I.202, A:L.203, A:A.247 Hydrogen bonds: C:E.65, A:F.135, A:R.137, A:R.137, A:M.138 Salt bridges: A:R.137 3PE.7: 19 residues within 4Å: Chain A: R.216, T.221, M.222, W.230, F.233, W.237, Y.318, V.325, F.328 Chain C: M.88, V.91 Chain D: K.23, T.24, G.27, M.31, A.35, I.39 Ligands: 3PE.11, 3PE.13 14 PLIP interactions: 10 interactions with chain A, 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: A:F.233, A:W.237, A:W.237, A:W.237, A:W.237, A:F.328, C:V.91, D:M.31, D:A.35, D:I.39 Hydrogen bonds: A:R.216, A:R.216, A:M.222 Salt bridges: A:H.223 3PE.10: 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: 3PE.6 18 PLIP interactions: 18 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, C:V.238 Hydrogen bonds: C:S.66, C:H.231, C:V.238, C:G.239 Salt bridges: 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, M.92, S.95, W.99, F.102, K.103, Y.107, P.114, V.252, V.253, F.256 Chain D: A.36 Ligands: 3PE.7, 3PE.12, 3PE.13 15 PLIP interactions: 5 interactions with chain A, 9 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.281, A:W.331, A:W.331, C:W.99, C:W.99, C:F.102, C:V.252, C:V.253, C:V.253, C:F.256, C:F.256 Hydrogen bonds: A:Q.344, B:R.209 Salt bridges: A:H.277, C:K.103 3PE.12: 11 residues within 4Å: Chain C: R.80, I.84, I.87, H.152, W.245, H.248 Chain D: F.25, V.32, T.33, V.37 Ligands: 3PE.11 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:V.32, C:I.84, C:I.87, C:W.245, C:W.245, C:H.248 Salt bridges: C:R.80 3PE.13: 18 residues within 4Å: Chain A: L.241, V.329, Q.344, Y.347, F.348 Chain C: M.92, Y.107, L.255, F.256, A.259 Chain D: I.39, L.43, L.46, A.47, N.50, A.51 Ligands: 3PE.7, 3PE.11 16 PLIP interactions: 6 interactions with chain A, 7 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: A:L.241, A:Y.347, A:Y.347, A:F.348, D:I.39, D:L.43, D:L.46, D:L.46, D:A.47, C:F.256, C:F.256, C:A.259 Hydrogen bonds: A:Q.344, D:N.50, D:A.51 Water bridges: A:S.341

Links

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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
G

B
H

C
I

D
J

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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