SMTL ID : 8jad.1

Crystal structure of Mycobacterium tuberculosis LpqY in complex with trehalose analogue YB-17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x YYD- GLC: alpha-D-glucopyranose-(1-1)-6-amino-6-deoxy-alpha-D-glucopyranose(Non-covalent)

YYD-GLC.1: 17 residues within 4Å: Chain A: P.40, T.42, D.43, R.71, P.73, Q.76, D.97, N.151, E.196, G.197, W.276, F.278, G.350, G.351, L.388, R.421 Ligands: BEZ.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.43, A:Q.76, A:N.151, A:D.97, A:N.151, A:G.351, A:G.351, A:R.421, A:R.421 Water bridges: A:Q.76, A:N.151

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.2: 5 residues within 4Å: Chain A: Q.191, G.197, W.276 Ligands: YYD-GLC.1, SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.191, A:Q.191

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

SO4.3: 4 residues within 4Å: Chain A: Q.191, S.260, R.262, F.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.260 Salt bridges: A:R.262 SO4.4: 3 residues within 4Å: Chain A: R.262, L.263, N.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.286 Salt bridges: A:R.262 SO4.5: 2 residues within 4Å: Chain A: R.361, H.362 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.362 SO4.6: 3 residues within 4Å: Chain A: S.72, N.74, E.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.72, A:S.72, A:N.74 SO4.7: 2 residues within 4Å: Chain A: L.78, R.82 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.82 SO4.8: 9 residues within 4Å: Chain A: Q.191, A.192, N.193, Q.194, G.195, E.196, G.197, L.198 Ligands: BEZ.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.193, A:N.193, A:N.193, A:Q.194, A:G.195, A:G.197, A:L.198

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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