- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 6 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)
- 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)
- 1 x CA: CALCIUM ION(Non-covalent)
- 1 x OH: HYDROXIDE ION(Non-covalent)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- 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)
- 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
AB
B - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 6 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)
- 3 x CU: COPPER (II) ION(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 1 x OH: HYDROXIDE ION(Non-covalent)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- 2 x HEA: HEME-A(Non-covalent)
- 11 x TRD: TRIDECANE(Non-covalent)(Non-functional Binders)
- 3 x CD: CADMIUM ION(Non-covalent)
- 1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 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
AB
B - Membrane
-
We predict this structure to be a membrane protein.