SMTL ID : 8b4o.1

Cryo-EM structure of cytochrome bd oxidase from C. glutamicum

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

HDD.1: 27 residues within 4Å: Chain A: D.54, E.57, V.58, I.61 Chain B: H.18, F.19, V.22, T.25, I.26, F.62, G.65, V.66, G.69, I.70, Q.72, E.73, F.76, F.103, E.106, S.107, T.136, S.139, A.140, I.143, A.186, W.400 Ligands: HEB.2 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:F.19, B:V.22, B:V.22, B:T.25, B:I.26, B:I.26, B:V.66, B:Q.72, B:F.76, B:F.76, B:F.103, B:F.103, B:F.103, B:A.140, B:I.143, B:I.143, B:A.186, B:W.400, A:I.61 Hydrogen bonds: B:E.106, B:E.106, B:E.106, B:S.107, B:S.139 Metal complexes: B:H.18

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

HEB.2: 20 residues within 4Å: Chain B: R.8, F.11, G.12, T.15, F.19, F.76, W.80, Y.83, F.91, I.143, A.146, N.147, M.150, W.400, E.404, M.405, R.407, Q.408, V.411 Ligands: HDD.1 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.11, B:F.11, B:F.19, B:F.76, B:Y.83, B:F.91, B:F.91, B:I.143, B:N.147, B:W.400, B:W.400, B:W.400, B:E.404, B:E.404, B:V.411 Hydrogen bonds: B:Q.408 Salt bridges: B:R.8, B:R.407 pi-Cation interactions: B:R.407, B:R.407 Metal complexes: B:E.404 HEB.3: 20 residues within 4Å: Chain B: F.19, A.182, H.185, G.189, L.192, L.245, G.249, Q.252, A.253, M.256, K.263, M.349, I.350, M.353, A.395, N.396, G.399, W.400, F.402, T.403 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.19, B:L.192, B:L.245, B:L.245, B:Q.252, B:A.253, B:I.350, B:I.350, B:M.353, B:A.395, B:W.400, B:W.400, B:W.400, B:F.402 Hydrogen bonds: B:Q.252, B:T.403, B:T.403 Salt bridges: B:K.263 pi-Stacking: B:W.400 pi-Cation interactions: B:H.185 Metal complexes: B:H.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grund, T.N. et al., Cryo-EM structure of cytochrome bd oxidase from C. glutamicum. To be published

Release Date

2022-12-28

Peptides

Cytochrome bd-type quinol oxidase subunit II: A
Cytochrome BD ubiquinol oxidase subunit I: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

We predict this structure to be a membrane protein.
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Cytochrome bd-type quinol oxidase subunit II

Cytochrome BD ubiquinol oxidase subunit I