SMTL ID : 7nkz.1

Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 A resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.1: 5 residues within 4Å: Chain B: E.98, F.103, S.139, I.143 Ligands: HDD.3 No protein-ligand interaction detected (PLIP)

1 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.2: 19 residues within 4Å: Chain B: R.8, W.9, G.12, V.16, Y.17, I.20, V.336, W.339, S.340, R.342, M.343, G.346, L.347, L.386, S.389, A.390, V.393, M.397 Ligands: HEB.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:R.8, B:V.16, B:Y.17, B:Y.17, B:I.20, B:W.339, B:W.339, B:W.339, B:R.342, B:M.343, B:L.347, B:L.386, B:A.390, B:V.393 pi-Stacking: B:W.9, B:W.9, B:W.9

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

HDD.3: 26 residues within 4Å: Chain A: D.59, E.62, V.63, I.66 Chain B: F.11, H.18, V.22, T.25, I.26, F.62, G.65, V.66, G.69, Q.72, E.73, F.76, F.103, E.106, S.107, S.139, A.140, I.143, I.144, T.186 Ligands: OXY.1, HEB.4 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:F.11, 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.103, B:F.103, B:A.140, B:I.143, B:I.144, B:T.186, A:I.66 Hydrogen bonds: B:S.107, B:S.139, A:E.62 Metal complexes: B:H.18

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

HEB.4: 22 residues within 4Å: Chain B: R.8, F.11, G.12, T.15, V.16, F.19, F.76, W.80, Y.83, F.91, I.143, N.147, M.150, W.392, E.396, M.397, R.399, Q.400, V.403, V.418 Ligands: MQ9.2, HDD.3 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:F.11, B:F.11, B:F.19, B:F.19, B:F.76, B:W.80, B:Y.83, B:F.91, B:I.143, B:I.143, B:N.147, B:W.392, B:W.392, B:W.392, B:W.392, B:E.396, B:V.403, B:V.418 Hydrogen bonds: B:Q.400 Salt bridges: B:R.8, B:R.8, B:R.399 pi-Cation interactions: B:R.399 Metal complexes: B:E.396 HEB.5: 21 residues within 4Å: Chain B: F.19, A.182, H.185, T.186, G.189, L.192, L.240, G.244, Q.247, G.248, M.251, K.258, M.344, I.345, M.348, A.387, N.388, G.391, W.392, F.394, T.395 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:F.19, B:L.240, B:Q.247, B:I.345, B:I.345, B:A.387, B:W.392, B:W.392, B:F.394 Hydrogen bonds: B:T.186, B:Q.247, B:T.395 Water bridges: B:Q.247 Salt bridges: B:K.258 pi-Stacking: B:H.185 pi-Cation interactions: B:H.185 Metal complexes: B:H.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safarian, S. et al., The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB. Nat Commun (2021)

Release Date

2021-09-22

Peptides

Probable integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB (Cytochrome BD-I oxidase subunit II): A
Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I 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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Probable integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB (Cytochrome BD-I oxidase subunit II)

Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I oxidase subunit I)

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