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

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

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

HEA.1: 36 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 33 PLIP interactions: 33 interactions with chain A, Hydrophobic interactions: A:V.45, A:T.48, A:I.99, A:M.106, A:V.110, A:V.111, A:A.114, A:V.429, A:V.429, A:I.432, A:I.436, A:T.467, A:F.468, A:F.468, A:F.468, A:A.501, A:F.508, A:F.508 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:T.48, 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.2: 29 residues within 4Å: Chain A: W.172, W.280, V.287, V.291, H.333, H.334, T.352, A.356, G.360, F.364, F.391, T.392, 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: P.83, I.86 Ligands: CYN.6 29 PLIP interactions: 27 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:V.291, A:T.352, A:F.364, A:F.391, A:F.391, A:V.396, A:I.399, A:L.401, A:V.416, A:F.420, A:F.420, A:V.423, A:V.423, A:M.424, B:P.83, B:I.86 Hydrogen bonds: A:W.172 Water bridges: A:Y.288, A:Y.288, A:D.412, A:D.412, A:R.481, A:R.482 Salt bridges: A:H.411, A:R.481 Metal complexes: A:H.419

3 x CU1: COPPER (I) ION(Non-covalent)

CU1.3: 4 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: CYN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.284, A:H.333, A:H.334 CU1.13: 5 residues within 4Å: Chain B: C.227, E.229, C.231, H.235 Ligands: CU1.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.227, B:E.229, B:C.231, B:H.235 CU1.14: 5 residues within 4Å: Chain B: H.192, C.227, C.231, M.238 Ligands: CU1.13 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: 3 residues within 4Å: Chain A: H.411, D.412 Chain B: 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.6, H2O.6, H2O.6

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 CYN: CYANIDE ION(Non-covalent)

CYN.6: 5 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: HEA.2, CU1.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.333 Water bridges: A:Y.288

6 x TRD: TRIDECANE(Non-covalent)

TRD.7: 5 residues within 4Å: Chain A: W.451, F.510, G.513, Y.517 Ligands: DMU.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.451, A:F.510, A:Y.517 TRD.10: 5 residues within 4Å: Chain A: M.53, L.80, W.81, P.82 Ligands: DMU.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.81, A:W.81, A:P.82 TRD.11: 1 residues within 4Å: Chain A: F.473 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.473 TRD.12: 3 residues within 4Å: Chain A: L.377, L.385, W.458 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.377, A:L.385, A:W.458, A:W.458 TRD.18: 8 residues within 4Å: Chain A: T.397, H.472, F.473, R.476 Chain B: T.16, G.17, I.40, T.44 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.397, A:F.473, B:I.40 TRD.19: 6 residues within 4Å: Chain A: M.350, M.353, V.354 Chain B: L.87, V.88, G.91 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.87, B:V.88, A:V.354

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

DMU.8: 2 residues within 4Å: Chain A: W.451 Ligands: TRD.7 No protein-ligand interaction detected (PLIP) DMU.9: 13 residues within 4Å: Chain A: V.49, M.53, M.56, A.57, Q.61, F.62, P.82, S.83, A.84, V.85, F.502, F.505 Ligands: TRD.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.49, A:F.502, A:F.502, A:F.505 Hydrogen bonds: A:S.83 Water bridges: A:A.57, A:A.57, A:P.58, A:Q.61, A:V.85 DMU.17: 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 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.46, B:F.46, B:L.50, B:L.75, B:W.79, B:W.79, A:F.364, A:F.364, A:I.367, A:W.371, A:W.371 Hydrogen bonds: B:H.71, B:N.72 DMU.20: 4 residues within 4Å: Chain B: P.96, F.99, N.100, E.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.103, B:E.103

2 x CD: CADMIUM ION(Non-covalent)

CD.15: 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.16: 2 residues within 4Å: Chain B: H.71, E.76 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.71, B:E.76, B:E.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, L. et al., Redox dependent conformational changes in cytochrome c oxidase suggest a gating mechanism for proton uptake. Biochemistry (2009)

Release Date

2009-06-16

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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