SMTL ID : 8jaa.1

Crystal structure of Mycobacterium tuberculosis LpqY in complex with trehalose analogue YB-04

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 9 residues within 4Å: Chain A: Q.191, A.192, N.193, Q.194, G.195, E.196, G.197, L.198 Ligands: TY6.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.191, A:N.193, A:N.193, A:G.195, A:E.196, A:G.197, A:L.198 Water bridges: A:Q.194, A:Q.194 SO4.2: 3 residues within 4Å: Chain A: S.260, R.262, F.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.260 Water bridges: A:R.262, A:R.262 Salt bridges: A:R.262 SO4.3: 2 residues within 4Å: Chain A: R.262, N.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.286, A:N.286 Salt bridges: A:R.262 SO4.4: 1 residues within 4Å: Chain A: H.362 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.362 SO4.5: 5 residues within 4Å: Chain A: P.117, R.361, H.362, R.363, A.364 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.363, A:A.364 Water bridges: A:H.362, A:E.365

2 x TY6: (2~{S},3~{R},4~{S},5~{S},6~{S})-6-[(2-azanylhydrazinyl)methyl]oxane-2,3,4,5-tetrol(Non-covalent)

TY6.6: 9 residues within 4Å: Chain A: P.40, T.42, D.43, R.71, Q.76, N.151, F.278, L.388 Ligands: TY6.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.43, A:D.43, A:Q.76 Water bridges: A:N.151, A:G.351 TY6.7: 11 residues within 4Å: Chain A: P.73, D.97, N.151, E.196, G.197, W.276, G.350, G.351, R.421 Ligands: SO4.1, TY6.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.97, A:N.151, A:G.197, A:G.351, A:R.421, A:R.421 Water bridges: A:E.196, A:E.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, J. et al., Molecular recognition of trehalose and trehalose analogues by Mycobacterium tuberculosis LpqY-SugABC. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-10-04

Peptides

Trehalose-binding lipoprotein LpqY: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Trehalose-binding lipoprotein LpqY

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