SMTL ID : 3eh4.1 (3 other biounits)

Structure of the reduced form of cytochrome ba3 oxidase from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CU1.1: 3 residues within 4Å: Chain A: H.289, H.338, H.339 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.289, A:H.338, A:H.339, H2O.2

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.2: 26 residues within 4Å: Chain A: L.88, G.95, P.96, Q.98, A.99, Y.102, Y.121, L.125, H.128, N.132, A.133, T.137, L.188, Y.189, F.441, H.442, V.445, A.446, T.450, W.484, M.488, M.491, R.505, R.506, A.507, L.533 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:L.88, A:Q.98, A:Y.102, A:N.132, A:A.133, A:T.137, A:Y.189, A:Y.189, A:F.441, A:V.445, A:A.446, A:W.484, A:W.484, A:L.533, A:L.533 Hydrogen bonds: A:R.506, A:A.507 Water bridges: A:Y.189, A:R.505, A:R.505 Salt bridges: A:R.505, A:R.506 pi-Stacking: A:F.441, A:H.442 Metal complexes: A:H.128, A:H.442

1 x HAS: HEME-AS(Non-covalent)

HAS.3: 33 residues within 4Å: Chain A: Y.189, W.285, V.292, Y.293, W.295, L.296, H.338, H.339, T.358, S.365, L.366, A.369, V.372, W.391, I.392, V.406, L.409, L.410, F.412, G.416, G.419, N.422, A.423, D.428, H.432, V.437, H.440, F.441, Q.444, V.445, R.505 Chain C: V.10, L.14 35 PLIP interactions: 33 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:W.285, A:V.292, A:V.292, A:W.295, A:L.296, A:T.358, A:L.366, A:A.369, A:V.372, A:W.391, A:I.392, A:I.392, A:V.406, A:L.409, A:L.410, A:F.412, A:F.412, A:F.412, A:N.422, A:F.441, A:F.441, A:Q.444, A:V.445, C:V.10, C:L.14 Hydrogen bonds: A:Y.293, A:Y.293 Water bridges: A:H.339, A:N.433, A:R.505 Salt bridges: A:H.432, A:R.505, A:R.506 pi-Cation interactions: A:H.289 Metal complexes: A:H.440

1 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.4: 6 residues within 4Å: Chain B: H.112, C.147, Q.149, C.151, H.155, M.158 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.112, B:C.147, B:C.147, B:Q.149, B:C.151, B:C.151, B:H.155

1 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.5: 6 residues within 4Å: Chain A: H.496, W.497, L.500, L.501, N.502 Chain C: R.32 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:H.496, A:W.497, A:W.497 Hydrogen bonds: C:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, B. et al., Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Biochemistry (2009)

Release Date

2009-04-21

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase polypeptide 2A: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase polypeptide 2A

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