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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

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

DMU.1: 3 residues within 4Å: Chain A: S.83, A.84, N.87 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.84, A:N.87 Water bridges: A:S.83, A:N.87 DMU.2: 2 residues within 4Å: Chain A: W.451 Ligands: TRD.12 No protein-ligand interaction detected (PLIP) DMU.3: 7 residues within 4Å: Chain A: W.20, V.31, L.34, M.443, S.444, L.512, L.519 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.512, A:L.519 Water bridges: A:M.443 DMU.4: 13 residues within 4Å: Chain A: V.49, M.53, M.56, A.57, Q.61, F.62, S.83, A.84, V.85, F.502, F.505 Ligands: TRD.13, TRD.19 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.49, A:F.502, A:F.502, A:F.505 Hydrogen bonds: A:A.57, A:S.83 Water bridges: A:M.53, A:P.58, A:Q.61, A:Q.61, A:V.85 DMU.20: 12 residues within 4Å: Chain A: F.364, I.367, A.368, W.371 Chain B: F.46, L.50, F.69, H.71, N.72, L.75, W.79 Ligands: TRD.28 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.46, B:L.50, B:L.75, B:W.79, B:W.79, A:F.364, A:I.367, A:A.368, A:W.371, A:W.371, A:W.371 Hydrogen bonds: B:N.72 DMU.21: 4 residues within 4Å: Chain B: L.95, P.96, F.99, E.103 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.103, B:E.103 Water bridges: B:E.103, B:E.103

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

CU.5: 4 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: OH.8 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.8 CU.22: 5 residues within 4Å: Chain B: C.227, E.229, C.231, H.235 Ligands: CU.23 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.227, B:E.229, B:C.231, B:H.235 CU.23: 5 residues within 4Å: Chain B: H.192, C.227, C.231, M.238 Ligands: CU.22 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.6: 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.7, H2O.8, H2O.8

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.8: 5 residues within 4Å: Chain A: H.284, V.287, H.334 Ligands: CU.5, HEA.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.283

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

PO4.9: 4 residues within 4Å: Chain A: F.135, P.136, R.137, M.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.137, A:M.138

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

HEA.10: 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 32 PLIP interactions: 32 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: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, A:F.511 Hydrogen bonds: A:T.48, A:R.52, A:W.172, A:Y.414, 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.11: 30 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, P.83 Ligands: OH.8 31 PLIP interactions: 1 interactions with chain B, 29 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.43, 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:V.416, A:F.420, A:F.420, A:V.423 Hydrogen bonds: A:W.172, A:Y.288 Water bridges: A:H.334, 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

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

TRD.12: 6 residues within 4Å: Chain A: P.449, W.451, F.510, G.513, Y.517 Ligands: DMU.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.449, A:F.510, A:Y.517, A:Y.517 TRD.13: 4 residues within 4Å: Chain A: L.80, W.81, P.82 Ligands: DMU.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.81, A:P.82 TRD.14: 6 residues within 4Å: Chain A: T.397, F.469, H.472, R.476 Chain B: T.16, G.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.397, A:F.469 TRD.15: 2 residues within 4Å: Chain A: F.469, W.493 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.469, A:W.493 TRD.16: 5 residues within 4Å: Chain A: L.377, L.385, G.386, F.389, W.458 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.377, A:L.385, A:F.389, A:W.458, A:W.458 TRD.17: 4 residues within 4Å: Chain A: Y.50, F.76, S.79, M.98 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.50, A:Y.50, A:F.76, A:F.76 TRD.18: 3 residues within 4Å: Chain A: W.331, T.343, Y.347 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.331, A:T.343, A:Y.347, A:Y.347 TRD.19: 1 residues within 4Å: Ligands: DMU.4 No protein-ligand interaction detected (PLIP) TRD.27: 6 residues within 4Å: Chain A: M.350, V.354 Chain B: L.87, V.88, G.91, A.92 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.354, B:L.87 TRD.28: 5 residues within 4Å: Chain A: F.364 Chain B: F.46, W.79, V.82 Ligands: DMU.20 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.364, B:F.46 TRD.29: 3 residues within 4Å: Chain A: A.65 Chain B: W.118, I.233 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.65, B:W.118

3 x CD: CADMIUM ION(Non-covalent)

CD.24: 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.25: 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.11, H2O.11 CD.26: 2 residues within 4Å: Chain B: H.259, H.261 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.259, B:H.261, H2O.11, H2O.12

1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.30: 4 residues within 4Å: Chain B: A.251, L.254, E.255, H.258 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.254, B:E.255 Hydrogen bonds: B:H.258

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
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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