SMTL ID : 3om3.2 (1 other biounit)

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with K362M mutation in the reduced state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

DMU.1: 11 residues within 4Å: Chain A: M.37, M.40, A.41, Q.45, F.46, P.66, S.67, A.68, V.69, F.486 Ligands: TRD.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.486, A:F.486 Hydrogen bonds: A:Q.45, A:Q.45, A:P.66 DMU.2: 1 residues within 4Å: Chain A: W.435 No protein-ligand interaction detected (PLIP) DMU.3: 3 residues within 4Å: Chain A: M.427, S.428, P.529 No protein-ligand interaction detected (PLIP) DMU.11: 5 residues within 4Å: Chain B: L.91, P.92, F.95, N.96, E.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.99, B:E.99 DMU.12: 4 residues within 4Å: Chain A: W.355 Chain B: F.65, H.67, N.68 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.355, B:H.67, B:N.68

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

HEA.4: 34 residues within 4Å: Chain A: L.18, G.22, V.29, T.32, M.35, R.36, W.79, I.83, H.86, 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, M.444, T.451, F.452, Q.455, R.465, R.466, Y.467, A.485, S.488, F.492 36 PLIP interactions: 36 interactions with chain A, Hydrophobic interactions: A:L.18, A:V.29, A:V.29, A:T.32, A:I.83, A:M.90, A:V.94, A:V.95, A:A.98, A:Y.398, A:V.401, A:V.413, A:V.413, A:I.416, A:T.451, A:F.452, A:F.452, A:F.452, A:A.485, A:F.492, A:F.492 Hydrogen bonds: A:T.32, A:R.36, A:W.156, A:Y.398, A:Q.455, A:R.466, A:Y.467 Water bridges: A:R.465, 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.5: 32 residues within 4Å: Chain A: W.156, W.264, V.271, Y.272, V.275, H.317, H.318, T.336, A.340, T.343, G.344, F.348, 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, V.43, P.79, I.82, L.83 32 PLIP interactions: 26 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:W.264, A:V.271, A:V.271, A:V.275, A:T.336, A:T.343, A:F.348, A:F.375, A:V.380, A:I.383, A:L.385, A:L.385, A:V.400, A:F.404, A:F.404, A:V.407, A:V.407, A:M.408, B:I.39, B:I.39, B:V.43, B:P.79, B:I.82, B:L.83 Hydrogen bonds: A:W.156, A:Y.272, A:T.343 Water bridges: A:D.396 Salt bridges: A:H.395, A:R.465 pi-Stacking: A:H.317 Metal complexes: A:H.403

3 x TRD: TRIDECANE(Non-covalent)

TRD.6: 4 residues within 4Å: Chain A: L.64, W.65, P.66 Ligands: DMU.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.65, A:W.65, A:P.66 TRD.7: 7 residues within 4Å: Chain A: F.453, H.456, F.457, R.460 Chain B: T.12, G.13, L.33 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.33, A:F.453, A:H.456, A:F.457 TRD.13: 3 residues within 4Å: Chain A: M.337 Chain B: G.87, L.91 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.91, A:M.337

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

CU1.8: 3 residues within 4Å: Chain A: H.268, H.317, H.318 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.268, A:H.317, A:H.318 CU1.14: 5 residues within 4Å: Chain B: C.223, E.225, C.227, H.231 Ligands: CU1.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.223, B:E.225, B:C.227, B:H.231 CU1.15: 5 residues within 4Å: Chain B: H.188, C.223, C.227, M.234 Ligands: CU1.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.188, B:C.223, B:C.227

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain A: H.395, D.396 Chain B: S.224, E.225 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.225, A:H.395, A:D.396, H2O.1, H2O.3

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 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.1

2 x CD: CADMIUM ION(Non-covalent)

CD.16: 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.17: 2 residues within 4Å: Chain B: H.67, E.72 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.67, B:E.72, B:E.72

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
C

B
D

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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