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

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with D132A mutation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-oligomer

Ligands

1 x OH: HYDROXIDE ION(Non-covalent)

OH.1: 5 residues within 4Å: Chain A: H.268, V.271, H.318 Ligands: HEA.8, CU.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.267

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

DMU.2: 6 residues within 4Å: Chain A: W.4, V.15, L.18, F.19, M.427, S.428 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.18, A:F.19, A:M.427 DMU.3: 8 residues within 4Å: Chain A: M.37, M.40, A.41, Q.45, F.46, F.486, F.489 Ligands: TRD.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.486, A:F.486, A:F.486, A:F.489 Hydrogen bonds: A:Q.45 Water bridges: A:A.41 DMU.15: 5 residues within 4Å: Chain B: Q.113, W.114, Y.115, P.135 Ligands: DMU.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.113, B:Q.113, B:W.114 DMU.16: 1 residues within 4Å: Ligands: DMU.15 No protein-ligand interaction detected (PLIP) DMU.17: 11 residues within 4Å: Chain A: F.348, I.351, A.352, W.355 Chain B: F.42, L.46, F.65, H.67, N.68, L.71, W.75 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.42, B:L.71, B:W.75, B:W.75, B:W.75, A:F.348, A:I.351, A:A.352, A:W.355, A:W.355, A:W.355 Hydrogen bonds: B:H.67, B:N.68 DMU.18: 4 residues within 4Å: Chain B: P.92, F.95, N.96, E.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.99, B:E.99

6 x TRD: TRIDECANE(Non-covalent)

TRD.4: 1 residues within 4Å: Chain A: F.453 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.453 TRD.5: 4 residues within 4Å: Chain A: A.30, Y.34, F.60, S.63 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.34, A:Y.34, A:F.60, A:F.60 TRD.6: 1 residues within 4Å: Chain A: L.483 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.483 TRD.9: 4 residues within 4Å: Chain A: L.64, W.65, P.66 Ligands: DMU.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.65, A:W.65, A:P.66 TRD.10: 7 residues within 4Å: Chain A: T.381, F.453, H.456, F.457, R.460 Chain B: T.12, T.40 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.381, A:F.453, A:H.456, A:F.457 TRD.19: 7 residues within 4Å: Chain A: M.334, M.337, V.338 Chain B: L.83, V.84, G.87, A.88 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.338, B:L.83

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

HEA.7: 38 residues within 4Å: Chain A: L.18, G.21, G.22, V.29, T.32, M.35, R.36, W.79, I.83, H.86, G.87, M.90, M.91, V.94, V.95, A.98, G.155, W.156, Y.398, V.401, F.404, H.405, M.408, S.409, V.413, I.416, I.420, M.444, T.451, F.452, Q.455, R.465, R.466, Y.467, A.485, S.488, F.492, F.495 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:V.29, A:T.32, A:I.83, A:M.90, A:V.95, A:A.98, A:V.401, A:F.404, A:M.408, A:V.413, A:I.416, A:I.420, A:T.451, A:F.452, A:A.485, A:F.492, A:F.492, A:F.495 Hydrogen bonds: A:T.32, A:R.36, A:W.156, A:Q.455, A:R.466, A:Y.467 Water bridges: A:R.465 Salt bridges: A:R.465, A:R.466 pi-Stacking: A:F.404, A:F.452 Metal complexes: A:H.86, A:H.405 HEA.8: 31 residues within 4Å: Chain A: W.156, W.264, V.271, Y.272, V.275, H.317, H.318, T.336, I.339, A.340, T.343, G.344, I.347, F.375, G.379, V.380, G.382, I.383, L.385, S.386, D.391, H.395, V.400, H.403, F.404, V.407, M.408, R.465 Chain B: I.39, P.79 Ligands: OH.1 35 PLIP interactions: 3 interactions with chain B, 31 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.39, B:I.39, B:P.79, A:W.264, A:V.271, A:V.271, A:V.271, A:V.275, A:V.275, A:T.336, A:A.340, A:T.343, A:I.347, A:F.375, A:I.383, A:L.385, A:L.385, A:V.400, A:F.404, A:F.404, A:V.407 Hydrogen bonds: A:W.156, A:Y.272 Water bridges: A:H.318, A:T.343, A:D.396, A:D.396, A:R.465, A:R.465 Salt bridges: A:H.395, A:R.465, A:R.466 pi-Cation interactions: A:H.268 Metal complexes: A:H.403, H2O.2

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

CU.11: 4 residues within 4Å: Chain A: H.268, H.317, H.318 Ligands: OH.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.268, A:H.317, A:H.318, OH.1, H2O.2 CU.21: 5 residues within 4Å: Chain B: C.223, E.225, C.227, H.231 Ligands: CU1.22 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.223, B:E.225, B:C.227, B:H.231

1 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 4 residues within 4Å: Chain A: H.395, D.396 Chain B: S.224, E.225 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.225, A:H.395, A:D.396, H2O.7, H2O.10, H2O.10

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 4 residues within 4Å: Chain A: E.38, A.41, G.43, Q.45 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.38, A:E.38, A:A.41, A:G.43, H2O.5

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 5 residues within 4Å: Chain A: T.8, N.9, H.10, A.116, M.117 Ligand excluded by PLIP

1 x HTH: (2S,3R)-heptane-1,2,3-triol(Non-covalent)

HTH.20: 5 residues within 4Å: Chain B: E.123, A.247, L.250, E.251, H.254 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.247, B:L.250, B:E.251 Hydrogen bonds: B:E.123

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

CU1.22: 5 residues within 4Å: Chain B: H.188, C.223, C.227, M.234 Ligands: CU.21 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.188, B:C.223, B:C.227

2 x CD: CADMIUM ION(Non-covalent)

CD.23: 3 residues within 4Å: Chain B: E.251, H.254, H.256 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.251, B:E.251, B:H.254, B:H.256 CD.24: 2 residues within 4Å: Chain B: H.67, E.72 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.67, B:E.72, H2O.7, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-02-02

Peptides

Cytochrome c oxidase, aa3 type, subunit I: 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, aa3 type, subunit I

Cytochrome c oxidase subunit 2

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