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

Catalytic Core (Subunits I and II) of Cytochrome c oxidase from Rhodobacter sphaeroides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

5 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.1: 7 residues within 4Å: Chain A: P.449, W.451, L.509, F.510, G.513, Y.517 Ligands: DMU.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.451, A:Y.517 Water bridges: A:Y.517 DMU.2: 5 residues within 4Å: Chain A: W.451, L.455, A.506, F.510 Ligands: DMU.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.455, A:F.510 DMU.3: 6 residues within 4Å: Chain A: W.20, V.31, L.34, F.35, M.443, S.444 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.35, A:F.35, A:M.443 Water bridges: A:M.443 DMU.15: 10 residues within 4Å: Chain A: F.364, I.367, W.371 Chain B: F.46, L.50, F.69, H.71, N.72, L.75, W.79 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.46, B:W.79, B:W.79, A:F.364, A:I.367, A:W.371, A:W.371 Hydrogen bonds: B:H.71, B:N.72 DMU.16: 4 residues within 4Å: Chain B: P.96, F.99, N.100, E.103 No protein-ligand interaction detected (PLIP)

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

CU.4: 4 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: OH.7 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.284, A:H.333, A:H.334, H2O.1, OH.7 CU.17: 5 residues within 4Å: Chain B: C.227, E.229, C.231, H.235 Ligands: CU.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.227, B:E.229, B:C.231, B:H.235 CU.18: 5 residues within 4Å: Chain B: H.192, C.227, C.231, M.238 Ligands: CU.17 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.5: 4 residues within 4Å: Chain A: H.411, D.412 Chain B: S.228, E.229 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.229, A:H.411, A:D.412, H2O.7, H2O.7, H2O.8

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: E.54, A.57, 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

1 x OH: HYDROXIDE ION(Non-covalent)

OH.7: 5 residues within 4Å: Chain A: H.284, V.287, H.334 Ligands: CU.4, HEA.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.283

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

HEA.8: 37 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, V.110, V.111, A.114, G.171, W.172, Y.414, V.417, F.420, H.421, M.424, S.425, V.429, I.432, M.460, T.467, F.468, Q.471, R.481, R.482, Y.483, A.501, S.504, F.508, F.511 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:V.45, A:T.48, A:I.99, A:M.106, A:V.111, A:A.114, A:V.417, A:F.420, A:M.424, A:V.429, A:V.429, A:I.432, A:T.467, A:F.468, A:A.501, A:F.508, A:F.511 Hydrogen bonds: A:T.48, A:R.52, A:W.172, A:Q.471, A:R.482, A:Y.483 Water bridges: A:R.481 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.9: 31 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, I.363, F.391, G.395, V.396, 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 Ligands: OH.7 32 PLIP interactions: 31 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:V.287, A:V.291, A:V.291, A:T.352, A:A.356, A:T.359, A:I.363, A:F.391, A:I.399, A:I.399, A:L.401, 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:T.359, A:D.412, A:D.412, A:R.481, A:R.481 Salt bridges: A:H.411, A:R.481, A:R.482 pi-Cation interactions: A:H.284 Metal complexes: A:H.419, H2O.1

6 x TRD: TRIDECANE(Non-covalent)(Non-functional Binders)

TRD.10: 4 residues within 4Å: Chain A: M.53, M.56, F.502 Ligands: TRD.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.502 TRD.11: 5 residues within 4Å: Chain A: M.53, L.80, W.81, P.82 Ligands: TRD.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.81, A:W.81, A:W.81, A:P.82 TRD.12: 6 residues within 4Å: Chain A: F.469, F.473, R.476 Chain B: T.16, G.17, T.44 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.473, B:T.44 TRD.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TRD.14: 2 residues within 4Å: Chain A: L.377 Chain B: H.59 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.377 TRD.21: 6 residues within 4Å: Chain A: M.350, V.354 Chain B: L.87, V.88, G.91, A.92 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.354

2 x CD: CADMIUM ION(Non-covalent)

CD.19: 3 residues within 4Å: Chain B: E.255, H.258, H.260 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.255, B:E.255, B:H.258, B:H.260 CD.20: 2 residues within 4Å: Chain B: H.71, E.76 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.71, B:E.76, B:E.76, H2O.10, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, L. et al., Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-10-10

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

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