SMTL ID : 9g2k.1

Cryo-EM structure of IrtAB in outward-occluded state in nanodisc in complex with ADP-vanadate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x AOV: ADP ORTHOVANADATE

AOV.1: 24 residues within 4Å: Chain A: T.412, Y.655, V.661, S.681, G.682, S.683, G.684, K.685, S.686, T.687, Q.727, E.807, H.838 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 22 PLIP interactions: 7 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:R.452, B:T.466, B:S.469, B:S.469, B:G.470, B:G.471, B:E.472, A:S.681, A:G.682, A:G.682, A:S.683, A:G.684, A:K.685, A:K.685, A:S.686, A:T.687, A:Q.727, A:E.807, A:H.838 Salt bridges: A:K.685 pi-Stacking: A:Y.655, A:Y.655 AOV.4: 25 residues within 4Å: Chain A: R.764, R.767, S.780, A.781, L.782, S.783, G.784, G.785, E.786, R.789, F.811 Chain B: Y.341, V.346, P.365, S.366, G.367, S.368, G.369, K.370, T.371, T.372, Q.412, E.493, H.524 Ligands: MG.5 23 PLIP interactions: 15 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:G.367, B:S.368, B:G.369, B:K.370, B:K.370, B:T.371, B:T.371, B:T.371, B:T.372, B:T.372, B:Q.412, B:Q.412, A:R.764, A:R.764, A:A.781, A:S.783, A:G.784, A:G.785, A:E.786, A:E.786 Salt bridges: B:K.370 pi-Stacking: B:Y.341, B:Y.341

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.686, Q.727 Chain B: S.469, G.470 Ligands: AOV.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.686 MG.5: 5 residues within 4Å: Chain B: T.371, Q.412, D.492, E.493 Ligands: AOV.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.371

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.385, H.431, T.435, H.436 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.385, A:H.431, A:H.436

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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