SMTL ID : 8vsi.1

Mechanistic Insights Revealed by YbtPQ in the Occluded State

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.384, Q.425 Ligands: AOV.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: T.385, Q.426 Ligands: AOV.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.385

2 x AOV: ADP ORTHOVANADATE

AOV.2: 24 residues within 4Å: Chain A: Q.116, Y.351, P.378, S.379, G.380, A.381, G.382, K.383, S.384, T.385, R.388, Y.393, Q.425, E.506, H.537 Chain B: G.480, Q.481, L.482, S.483, G.484, G.485, E.486, A.511 Ligands: MG.1 25 PLIP interactions: 18 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Q.116, A:Q.116, A:P.378, A:G.380, A:A.381, A:G.382, A:K.383, A:K.383, A:S.384, A:S.384, A:T.385, A:T.385, A:R.388, A:E.506, B:Q.481, B:S.483, B:S.483, B:G.484, B:G.485, B:E.486, B:A.511 Salt bridges: A:K.383, A:R.388 pi-Stacking: A:Y.351, A:Y.351 AOV.4: 23 residues within 4Å: Chain A: V.479, F.480, L.481, S.482, G.483, G.484, Q.485, F.510 Chain B: Y.353, A.379, S.380, G.381, A.382, G.383, K.384, T.385, T.386, K.389, Y.394, Q.426, E.507, H.538 Ligands: MG.3 24 PLIP interactions: 7 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:S.482, A:S.482, A:G.483, A:G.484, A:Q.485, A:Q.485, A:F.510, B:A.379, B:G.381, B:A.382, B:G.383, B:K.384, B:K.384, B:T.385, B:T.385, B:T.386, B:T.386, B:K.389, B:K.389, B:Y.394, B:Q.426 Salt bridges: B:K.384 pi-Stacking: B:Y.353, B:Y.353

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, W. et al., Mechanistic Insights Revealed by YbtPQ in the Occluded State. Biomolecules (2024)

Release Date

2024-04-10

Peptides

ABC transporter ATP-binding protein: A
Permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtQ: 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

Permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtQ

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