SMTL ID : 3dtu.2 (1 other biounit)

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides complexed with deoxycholic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

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

DMU.1: 10 residues within 4Å: Chain A: M.53, M.56, A.57, Q.61, F.62, S.83, A.84, V.85, F.502, F.505 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.502, A:F.505 Hydrogen bonds: A:S.83 Water bridges: A:M.53, A:A.57, A:P.58, A:Q.61, A:V.85 DMU.2: 6 residues within 4Å: Chain A: L.314, Y.318, V.321, A.322 Chain B: H.71 Ligands: DXC.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.318, A:Y.318, A:V.321 DMU.19: 5 residues within 4Å: Chain A: M.350 Chain B: P.96, F.99, N.100, E.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.103, B:E.103, B:E.103

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

CU.3: 4 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: OH.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.284, A:H.333, A:H.334, OH.6 CU.20: 5 residues within 4Å: Chain B: C.227, E.229, C.231, H.235 Ligands: CU.21 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.227, B:E.229, B:C.231, B:H.235 CU.21: 5 residues within 4Å: Chain B: H.192, C.227, C.231, M.238 Ligands: CU.20 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.4: 4 residues within 4Å: Chain A: H.411, D.412 Chain B: S.228, E.229 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.411, A:D.412, B:E.229, H2O.2, H2O.8, H2O.9

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.6: 6 residues within 4Å: Chain A: H.284, V.287, H.333, H.334 Ligands: CU.3, HEA.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.283

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 5 residues within 4Å: Chain A: A.134, F.135, P.136, R.137, M.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.137, A:M.138 Salt bridges: A:R.137

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, 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, Y.483, A.501, S.504, F.508, F.511 31 PLIP interactions: 31 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:Y.414, 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, 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: 29 residues within 4Å: Chain A: 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, 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.6 33 PLIP interactions: 31 interactions with chain A, 1 interactions with chain B, 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:L.401, A:L.401, A:V.416, A:F.420, A:F.420, A:V.423, B:I.43 Hydrogen bonds: A:W.172, A:Y.288, 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

1 x DXC: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID(Non-covalent)

DXC.10: 11 residues within 4Å: Chain A: P.315, Y.318, A.319, A.322, P.358, I.361 Chain B: H.71, E.76, T.80 Ligands: DMU.2, CD.23 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.318, A:I.361, B:E.76, B:T.80 Hydrogen bonds: A:Y.318 Salt bridges: B:H.71

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

TRD.11: 7 residues within 4Å: Chain A: W.20, V.31, L.34, F.35, M.443, S.444, L.519 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.20, A:V.31, A:F.35, A:L.519 TRD.12: 6 residues within 4Å: Chain A: L.377, L.385, G.386, F.389, W.458 Chain B: L.52 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.52, A:L.377, A:L.385, A:F.389, A:W.458, A:W.458 TRD.13: 5 residues within 4Å: Chain A: Y.50, F.76, S.79, L.80, M.98 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.50, A:Y.50, A:L.80 TRD.14: 2 residues within 4Å: Chain A: W.331, Y.347 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.331, A:Y.347, A:Y.347 TRD.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TRD.16: 1 residues within 4Å: Chain A: W.371 No protein-ligand interaction detected (PLIP) TRD.17: 5 residues within 4Å: Chain A: H.223, K.224, Y.313, D.536, T.537 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.313, A:Y.313, A:T.537 TRD.18: 12 residues within 4Å: Chain A: H.127, H.300, A.303, T.304, F.438, W.439, H.534, A.535, D.536, T.537, E.539, W.540 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.300, A:A.303, A:F.438, A:F.438, A:W.439, A:T.537 TRD.24: 9 residues within 4Å: Chain A: T.397, F.469, H.472, F.473, R.476 Chain B: T.16, G.17, L.37, T.44 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.397, A:F.469, A:H.472, A:F.473, B:L.37 TRD.25: 6 residues within 4Å: Chain A: M.350 Chain B: L.87, V.88, G.91, A.92, L.95 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.87, B:L.95 TRD.26: 4 residues within 4Å: Chain A: F.364 Chain B: I.43, F.46, V.82 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.43, B:F.46, B:F.46, B:V.82, B:V.82 TRD.27: 1 residues within 4Å: Chain B: Y.53 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.53, B:Y.53

2 x CD: CADMIUM ION(Non-covalent)

CD.22: 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.23: 3 residues within 4Å: Chain B: H.71, E.76 Ligands: DXC.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.71, B:E.76, B:E.76, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, L. et al., A conserved steroid binding site in cytochrome C oxidase. Biochemistry (2008)

Release Date

2008-09-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

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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