SMTL ID : 2qpd.1

An unexpected outcome of surface-engineering an integral membrane protein: Improved crystallization of cytochrome ba3 oxidase from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 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: 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: 24 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, 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:A.49, A:Y.52, A:L.75, A:N.82, A:A.83, A:Y.139, A:Y.139, A:F.391, A:F.391, A:V.395, A:A.396, A:L.483, A:L.483 Hydrogen bonds: A:Y.139, A:R.456, A:A.457 Salt bridges: A:R.455, A:R.456 Metal complexes: 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, Y.250, H.288, H.289, T.308, A.312, S.315, L.316, A.319, A.323, L.326, 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: L.15 Ligands: CU1.1 32 PLIP interactions: 31 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:V.242, A:V.242, A:W.245, A:L.246, A:L.246, A:T.308, A:L.316, A:A.319, A:A.323, A:L.326, A:V.356, A:L.359, A:L.359, A:L.360, A:F.362, A:F.362, A:I.363, A:A.373, A:V.387, A:F.391, A:F.391, A:Q.394, A:Q.394, A:V.395, C:L.15 Hydrogen bonds: A:Y.243, A:Y.243 Salt bridges: A:H.382, A:R.455, A:R.456 pi-Cation interactions: A:H.239 Metal complexes: A:H.390

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

CUA.4: 7 residues within 4Å: Chain B: H.114, C.149, Q.151, Y.152, 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., An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus. Acta Crystallogr.,Sect.F (2007)

Release Date

2007-12-11

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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