SMTL ID : 9g2x.1

Cryo-EM structure of IrtAB in outward-occluded state in presence of mycobactin under turnover conditions in LMNG

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: T.107, Y.350, R.351, V.356, S.376, G.377, S.378, G.379, K.380, S.381, T.382, Q.422, H.533 Chain B: R.452, L.453, T.466, A.467, L.468, S.469, G.470, G.471, E.472, A.497 Ligands: MG.2 25 PLIP interactions: 19 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:T.107, A:Y.350, A:R.351, A:S.376, A:G.377, A:S.378, A:G.379, A:K.380, A:S.381, A:T.382, A:Q.422, B:R.452, B:S.469, B:G.470, B:G.471, B:E.472, B:A.497 Water bridges: A:S.381, A:E.502, A:E.502 Salt bridges: A:K.380, A:K.380, A:H.533 pi-Stacking: A:Y.350, A:Y.350 ATP.4: 22 residues within 4Å: Chain A: R.459, G.474, S.475, A.476, L.477, S.478, G.479, G.480, E.481 Chain B: Y.341, E.344, V.346, S.366, G.367, S.368, G.369, K.370, T.371, T.372, Q.412, H.524 Ligands: MG.5 27 PLIP interactions: 10 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:R.459, A:R.459, A:G.474, A:A.476, A:S.478, A:S.478, A:G.479, A:G.480, A:E.481, A:E.481, B:S.366, B:G.367, B:S.368, B:G.369, B:K.370, B:T.371, B:T.372, B:Q.412 Water bridges: B:T.371, B:T.371, B:E.493, B:E.493 Salt bridges: B:K.370, B:K.370, B:H.524 pi-Stacking: B:Y.341, B:Y.341

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: S.381, Q.422, D.501, E.502 Chain B: G.470 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.381, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain B: K.370, T.371, Q.412 Ligands: ATP.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.371, H2O.1, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.80, H.126, H.131 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.80, A:H.126, A:H.131, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonda, I. et al., The mycobacterial ABC transporter IrtAB employs a membrane-facing crevice for siderophore-mediated iron uptake. Nature (2024)

Release Date

2024-12-18

Peptides

Mycobactin import ATP-binding/permease protein IrtA: A
Mycobactin import ATP-binding/permease protein IrtB: 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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Mycobactin import ATP-binding/permease protein IrtA

Mycobactin import ATP-binding/permease protein IrtB

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