SMTL ID : 9fka.1

Cryo-EM structure of the reduced cytochrome bd oxidase from M. tuberculosis

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.96 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 6 residues within 4Å: Chain A: R.8, W.9, D.329, N.333, V.336 Ligands: MQ9.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.9, A:V.336 Salt bridges: A:R.8

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

MQ9.2: 16 residues within 4Å: Chain A: R.8, W.9, G.12, I.13, V.16, Y.17, V.336, W.339, M.343, G.346, L.386, S.389, A.390, M.397 Ligands: PTY.1, HEM.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.8, A:I.13, A:V.16, A:V.16, A:Y.17, A:W.339, A:M.343, A:L.386, A:A.390 pi-Stacking: A:W.9, A:W.9, A:W.9

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

HEM.3: 19 residues within 4Å: Chain A: R.8, F.11, G.12, T.15, V.16, F.19, F.76, W.80, F.91, I.143, N.147, M.150, W.392, E.396, R.399, Q.400, V.418 Ligands: MQ9.2, HDD.5 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:T.15, A:V.16, A:F.19, A:F.76, A:W.80, A:F.91, A:I.143, A:N.147, A:W.392, A:W.392, A:E.396 Hydrogen bonds: A:Q.400 Salt bridges: A:R.8, A:R.399 pi-Stacking: A:F.11 pi-Cation interactions: A:R.399 Metal complexes: A:E.396 HEM.4: 20 residues within 4Å: Chain A: A.182, H.185, T.186, G.189, L.192, L.240, L.241, G.244, Q.247, M.251, K.258, M.344, I.345, M.348, A.387, N.388, G.391, W.392, F.394, T.395 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:L.192, A:L.240, A:L.241, A:Q.247, A:I.345, A:A.387, A:W.392, A:F.394, A:T.395 Salt bridges: A:K.258 Metal complexes: A:H.185

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

HDD.5: 23 residues within 4Å: Chain A: H.18, F.19, V.22, T.25, I.26, F.62, V.66, G.69, I.70, Q.72, E.73, F.103, E.106, S.107, S.139, A.140, I.143, I.144, T.186 Chain B: E.62, V.63, I.66 Ligands: HEM.3 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:F.19, A:V.22, A:V.22, A:T.25, A:I.26, A:I.26, A:Q.72, A:F.103, A:F.103, A:F.103, A:A.140, A:I.143, A:I.144, A:T.186, B:I.66 Hydrogen bonds: A:E.106, A:S.107, A:S.139, B:E.62 Metal complexes: A:H.18

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.6: 20 residues within 4Å: Chain B: A.13, G.17, I.20, L.21, W.64, L.187, K.188, S.251, D.252, G.253, W.254, F.256, M.257, L.260, V.316, T.320, Y.323, W.324, R.327, R.329 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.20, B:W.64, B:L.187, B:W.254, B:F.256, B:L.260, B:L.260, B:T.320, B:T.320, B:Y.323 Hydrogen bonds: B:S.251, B:D.252, B:G.253, B:W.254, B:R.329 Salt bridges: B:K.188, B:R.329

1 x CD4: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate(Non-covalent)

CD4.7: 6 residues within 4Å: Chain B: E.5, V.10, A.12, A.13, W.227, Y.275 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:E.5, B:V.10, B:A.12, B:A.13, B:W.227, B:W.227, B:W.227, B:Y.275, B:Y.275 Hydrogen bonds: B:Y.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van der Velden, T.T. et al., Menaquinone-specific turnover by Mycobacterium tuberculosis cytochrome bd is redox regulated by the Q-loop disulfide bond. J.Biol.Chem. (2024)

Release Date

2025-02-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I oxidase subunit I)

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

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