SMTL ID : 3qjr.1

The structure of and photolytic induced changes of carbon monoxide binding to the cytochrome ba3-oxidase from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CU1.1: 4 residues within 4Å: Chain A: H.239, H.288, H.289 Ligands: CMO.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.239, A:H.288, A:H.289, CMO.4

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 28 residues within 4Å: Chain A: L.38, S.42, G.45, P.46, Q.48, A.49, Y.52, Y.71, L.75, H.78, G.79, N.82, A.83, F.86, L.138, Y.139, F.391, H.392, V.395, A.396, T.400, W.434, M.438, M.441, R.455, R.456, A.457, L.483 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:L.38, A:Q.48, A:Y.52, A:N.82, A:A.83, A:F.86, A:Y.139, A:F.391, A:V.395, A:A.396, A:W.434, A:L.483 Hydrogen bonds: A:R.456, A:A.457 Salt bridges: A:R.455, A:R.456 pi-Stacking: A:F.391 pi-Cation interactions: A:H.392 Metal complexes: A:H.78, A:H.392

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

HAS.3: 36 residues within 4Å: Chain A: Y.139, W.235, V.242, Y.243, W.245, L.246, H.288, H.289, T.308, S.315, L.316, A.319, A.323, W.341, V.356, L.359, L.360, F.362, I.363, G.366, G.369, I.370, N.372, A.373, D.378, H.382, V.387, H.390, F.391, Q.394, V.395, R.455, R.456 Chain C: V.11, L.15 Ligands: CMO.4 35 PLIP interactions: 33 interactions with chain A, 1 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.235, A:V.242, A:V.242, A:W.245, A:W.245, A:L.246, A:T.308, A:L.316, A:A.319, A:A.323, A:W.341, A:V.356, A:L.359, A:L.359, A:L.360, A:F.362, A:I.363, A:N.372, A:V.387, A:V.387, A:F.391, A:F.391, A:Q.394, A:V.395, C:V.11 Hydrogen bonds: A:Y.139, A:Y.243, A:Y.243 Salt bridges: A:H.382, A:R.455, A:R.456 pi-Stacking: A:H.289 pi-Cation interactions: A:H.239 Metal complexes: A:H.390, CMO.4

1 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.4: 5 residues within 4Å: Chain A: H.239, H.288, H.289 Ligands: CU1.1, HAS.3 No protein-ligand interaction detected (PLIP)

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

CUA.5: 6 residues within 4Å: Chain B: H.114, C.149, Q.151, C.153, H.157, M.160 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.114, B:C.149, B:C.149, B:Q.151, B:C.153, B:C.153, B:H.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, B. et al., Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to Cu(B). Biochim.Biophys.Acta (2012)

Release Date

2012-01-25

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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