SMTL ID : 5doq.1

The structure of bd oxidase from Geobacillus thermodenitrificans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x HEB: HEME B/C(Non-covalent)

HEB.1: 19 residues within 4Å: Chain A: K.183, H.186, T.190, M.193, G.238, D.239, S.241, G.242, L.245, K.252, M.325, V.326, G.329, A.366, A.369, I.370, G.373, W.374, A.377 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:T.190, A:V.326, A:V.326, A:A.369, A:I.370, A:W.374, A:W.374, A:W.374 Salt bridges: A:K.183, A:K.183, A:K.252 pi-Stacking: A:H.186, A:H.186 pi-Cation interactions: A:H.186 Metal complexes: A:H.186 HEB.2: 21 residues within 4Å: Chain A: H.21, Y.24, A.25, V.65, G.68, V.69, G.72, T.73, I.75, G.76, L.98, E.101, T.102, F.105, A.143, I.146, V.187 Chain B: N.60, V.61, V.64 Ligands: HDD.3 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:A.25, A:I.75, A:L.98, A:T.102, A:F.105, A:F.105, A:A.143, A:I.146, A:I.146, A:I.146, A:V.187, B:V.64 pi-Stacking: A:H.21, A:H.21 Metal complexes: A:H.21, A:E.101

1 x HDD: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE(Non-covalent)

HDD.3: 17 residues within 4Å: Chain A: R.11, E.15, L.18, T.19, I.22, W.83, I.146, T.147, V.149, N.150, M.153, W.374, Y.375, E.378, R.381, Q.382 Ligands: HEB.2 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:R.11, A:E.15, A:L.18, A:I.22, A:W.83, A:V.149, A:N.150, A:W.374, A:Y.375, A:Y.375, A:E.378 Hydrogen bonds: A:N.150 pi-Cation interactions: A:R.381 Metal complexes: A:E.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safarian, S. et al., Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases. Science (2016)

Release Date

2016-05-04

Peptides

Bd-type quinol oxidase subunit I: A
Bd-type quinol oxidase subunit II: B
Putative membrane protein: 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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Bd-type quinol oxidase subunit I

Bd-type quinol oxidase subunit II

Putative membrane protein

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