SMTL ID : 3s3d.1

Structure of Thermus thermophilus cytochrome ba3 oxidase 480s after Xe depressurization

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.75 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.239, H.288, H.289 Ligands: HAS.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.239, A:H.288, A:H.289

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

HEM.2: 26 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, N.82, A.83, 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:Y.52, A:N.82, A:A.83, A:Y.139, A:F.391, A:F.391, A:V.395, A:V.395, A:A.396, A:W.434, A:L.483 Hydrogen bonds: A:Y.52, A:Y.71, A:R.456, A:A.457 Salt bridges: A:R.455, A:R.456 Metal complexes: A:H.78, A:H.392

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

HAS.3: 35 residues within 4Å: Chain A: Y.139, W.235, V.242, Y.243, W.245, L.246, Y.250, H.288, H.289, T.308, S.315, A.319, A.323, W.341, I.342, 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 Chain C: V.10 Ligands: CU.1 35 PLIP interactions: 33 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:W.235, A:V.242, A:V.242, A:W.245, A:W.245, A:L.246, A:T.308, A:A.319, A:A.323, A:W.341, A:I.342, A:L.359, A:L.360, A:F.362, A:F.362, A:F.362, A:I.363, A:I.363, A:I.370, A:N.372, A:A.373, A:V.387, A:F.391, A:F.391, A:Q.394, A:V.395, C:V.10, C:V.10 Hydrogen bonds: A:Y.243 Salt bridges: A:H.382, A:R.455, A:R.456 pi-Cation interactions: A:H.239, A:H.289 Metal complexes: A:H.390

3 x XE: XENON(Non-covalent)(Non-functional Binders)

XE.4: 2 residues within 4Å: Chain A: Y.139, G.238 No protein-ligand interaction detected (PLIP) XE.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) XE.6: 1 residues within 4Å: Chain A: Y.152 No protein-ligand interaction detected (PLIP)

1 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.7: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luna, V.M. et al., Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase. Biochemistry (2012)

Release Date

2012-05-23

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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