SMTL ID : 8jab.1

Crystal structure of Mycobacterium tuberculosis LpqY in complex with trehalose analogue YB-06

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x U0X: (2~{S},3~{S},4~{R},5~{S},6~{R})-2-(fluoranylmethyl)-6-[(2~{R},3~{R},4~{S},5~{S},6~{S})-6-(fluoranylmethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-oxane-3,4,5-triol(Non-covalent)

U0X.1: 16 residues within 4Å: Chain A: P.40, T.42, D.43, P.73, Q.76, D.97, N.151, E.196, G.197, V.200, W.276, F.278, G.350, G.351, L.388, R.421 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.76, A:D.97, A:N.151, A:G.351, A:R.421, A:R.421 Water bridges: A:D.43, A:Q.76

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

SO4.2: 10 residues within 4Å: Chain A: R.71, Q.191, A.192, N.193, Q.194, G.195, E.196, G.197, L.198, E.258 11 PLIP interactions: 11 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:R.71, A:Q.194, A:Q.194 Salt bridges: A:R.71 SO4.3: 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 SO4.4: 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 SO4.5: 2 residues within 4Å: Chain A: N.298, R.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.298 Salt bridges: A:R.299 SO4.6: 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:H.362

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

2023-09-27

Peptides

Trehalose-binding lipoprotein LpqY: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Trehalose-binding lipoprotein LpqY

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