SMTL ID : 9iqg.1

Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the ATP|ADP+Vi-bound Occ (Vi) state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: Y.355, V.362, S.381, T.382, G.383, S.384, G.385, K.386, S.387, T.388, Q.428 Chain B: L.513, G.526, A.527, I.528, S.529, A.530, G.531, E.532, S.557 Ligands: MG.2 19 PLIP interactions: 6 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:S.529, B:A.530, B:G.531, B:E.532, B:E.532, B:S.557, A:G.383, A:G.383, A:S.384, A:G.385, A:K.386, A:S.387, A:T.388, A:T.388, A:Q.428 Salt bridges: A:K.386, A:K.386 pi-Stacking: A:Y.355, A:Y.355

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.387, Q.428 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.387 MG.5: 4 residues within 4Å: Chain B: T.431, Q.472 Ligands: ADP.3, VO4.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.431

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 18 residues within 4Å: Chain A: I.482, N.483, F.484, S.485, Q.488 Chain B: D.166, Y.400, P.425, T.426, G.427, A.428, G.429, K.430, T.431, T.432, Y.441 Ligands: VO4.4, MG.5 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.166, B:P.425, B:A.428, B:G.429, B:K.430, B:T.431, B:T.432, B:T.432, A:R.217, A:S.485, A:S.485, A:Q.488, A:Q.488 Salt bridges: B:K.430 pi-Stacking: B:Y.400, B:Y.400

1 x VO4: VANADATE ION(Non-covalent)

VO4.4: 14 residues within 4Å: Chain A: S.485, G.486, G.487, Q.488, A.513 Chain B: P.425, T.426, K.430, T.431, Q.472, E.553, H.584 Ligands: ADP.3, MG.5 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.486, A:G.487, A:Q.488, A:A.513, A:A.513, B:K.430, B:Q.472

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, J. et al., Structure and mechanism of a mycobacterial isoniazid efflux pump MsRv1273c/72c with a degenerate nucleotide-binding site. Nat Commun (2025)

Release Date

2025-05-14

Peptides

ABC transporter, ATP-binding protein: A
ABC transporter transmembrane region: 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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ABC transporter, ATP-binding protein

ABC transporter transmembrane region

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