SMTL ID : 1xme.1

Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

BNG.1: 5 residues within 4Å: Chain A: K.25, Y.29, W.113, L.114, W.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.25, A:K.25

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

CU.2: 4 residues within 4Å: Chain A: H.239, H.288, H.289 Ligands: HAS.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.239, A:H.288, A:H.289, H2O.3

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

HEM.3: 26 residues within 4Å: Chain A: L.38, G.45, P.46, Q.48, A.49, Y.52, Y.71, L.75, H.78, G.79, 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 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:L.38, A:Q.48, A:Y.52, A:N.82, A:A.83, 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 Water bridges: A:Y.139, A:R.455, A:R.455 Salt bridges: A:R.455, A:R.456 pi-Stacking: A:F.391 Metal complexes: A:H.78, A:H.392

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

HAS.4: 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, I.342, V.356, L.359, L.360, F.362, 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.11, L.15 Ligands: CU.2, GOL.5 40 PLIP interactions: 37 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.235, A:V.242, 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:I.342, A:V.356, A:L.359, A:L.359, A:L.360, A:F.362, A:F.362, A:N.372, A:A.373, A:V.387, A:F.391, A:F.391, A:Q.394, A:V.395, C:V.11, C:L.15 Hydrogen bonds: A:Y.139, A:Y.243, A:Y.243 Water bridges: A:R.455, A:R.455, A:R.455 Salt bridges: A:H.382, A:R.455, A:R.456 pi-Cation interactions: A:H.239 Metal complexes: A:H.390, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain A: T.140, Y.142, R.231, H.289, H.382, N.383, R.455, R.456 Chain B: E.126, Q.151 Ligands: HAS.4 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.142, A:R.231, A:R.231, A:H.382, B:Q.151 Water bridges: A:H.289, A:R.455

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

CUA.6: 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

Hunsicker-Wang, L.M. et al., A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-03-22

Peptides

Cytochrome c oxidase polypeptide I: A
Cytochrome c oxidase polypeptide II: B
Cytochrome c oxidase polypeptide IIA: 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 polypeptide I

Cytochrome c oxidase polypeptide II

Cytochrome c oxidase polypeptide IIA

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