SMTL ID : 8jac.1

Crystal structure of Mycobacterium tuberculosis LpqY in complex with trehalose analogue YB-16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.71, Q.191, S.260, R.262, F.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.260 Water bridges: A:A.261 Salt bridges: A:R.71, A:R.262 SO4.2: 9 residues within 4Å: Chain A: Q.191, A.192, N.193, Q.194, G.195, E.196, G.197, L.198 Ligands: W4Z.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.191, A:N.193, A:Q.194, A:G.195, A:G.197, A:L.198 Water bridges: A:E.196, A:E.196, A:E.196 SO4.3: 1 residues within 4Å: Chain A: H.362 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.361 Salt bridges: A:H.362 SO4.4: 3 residues within 4Å: Chain A: R.262, L.263, N.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.286, A:N.286 Salt bridges: A:R.262

1 x W4Z: N-[[(2R,3S,4S,5R,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl]ethanamide(Non-covalent)

W4Z.5: 12 residues within 4Å: Chain A: P.73, D.97, N.151, Q.191, E.196, G.197, W.276, G.350, G.351, R.421 Ligands: SO4.2, GLC.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Q.191 Hydrogen bonds: A:D.97, A:N.151, A:G.351, A:R.421, A:R.421 Water bridges: A:Q.76, A:E.196

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.6: 10 residues within 4Å: Chain A: P.40, T.42, D.43, R.71, Q.76, N.151, W.276, F.278, L.388 Ligands: W4Z.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.43, A:Q.76, A:N.151 Water bridges: A:Q.76, A:N.151

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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