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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x OH: HYDROXIDE ION(Non-covalent)

OH.1: 5 residues within 4Å: Chain A: H.268, V.271, H.318 Ligands: HEA.7, CU1.11 No protein-ligand interaction detected (PLIP)

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

DMU.2: 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.3: 6 residues within 4Å: Chain A: W.4, V.15, F.19, M.427, S.428, I.499 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.19, A:M.427, A:I.499 DMU.15: 5 residues within 4Å: Chain B: Q.113, W.114, Y.115, P.135 Ligands: DMU.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.113, B:Q.113, B:W.114 Water bridges: B:Q.113, B:Q.113 DMU.16: 1 residues within 4Å: Ligands: DMU.15 No protein-ligand interaction detected (PLIP) DMU.17: 10 residues within 4Å: Chain A: F.348, A.352, W.355 Chain B: F.42, L.46, F.65, H.67, N.68, L.71, W.75 12 PLIP interactions: 7 interactions with chain B, 5 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: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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.99

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

TRD.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TRD.5: 4 residues within 4Å: Chain A: A.30, Y.34, F.60, S.63 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.34, A:Y.34, A:Y.34, A:F.60, A:F.60 TRD.8: 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.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.65 TRD.10: 9 residues within 4Å: Chain A: V.380, T.381, F.453, H.456, F.457, R.460 Chain B: T.12, L.33, T.40 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.33, B:L.33, A:V.380, A:T.381, A:F.453, A:F.457 TRD.19: 4 residues within 4Å: Chain A: M.337, V.338 Chain B: L.83, V.84 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.338, B:L.83, B:V.84

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

HEA.6: 37 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, 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 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:V.29, A:T.32, A:I.83, A:M.90, A:V.95, A:V.401, A:F.404, A:M.408, A:V.413, 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.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.7: 29 residues within 4Å: Chain A: W.156, W.264, V.271, Y.272, V.275, H.317, H.318, T.336, 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 26 PLIP interactions: 2 interactions with chain B, 23 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.39, B:P.79, A:W.264, A:V.271, A:V.271, A:V.271, A:V.275, A:T.336, A:T.343, A:I.347, A:F.375, A:L.385, A:V.400, A:F.404, A:F.404, A:V.407 Hydrogen bonds: A:W.156 Water bridges: A:D.396, A:R.465, A:R.465, A:R.466 Salt bridges: A:H.395, A:R.465, A:R.466 pi-Cation interactions: A:H.268 Metal complexes: H2O.1

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

CU1.11: 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-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.268, A:H.317, A:H.318, H2O.1, OH.1 CU1.21: 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 CU1.22: 5 residues within 4Å: Chain B: H.188, C.223, C.227, M.234 Ligands: CU1.21 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.12: 3 residues within 4Å: Chain A: H.395, D.396 Chain B: 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.4, H2O.7, 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.4

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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.250, B:E.251 Hydrogen bonds: B:E.123

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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