SMTL ID : 8ja9.1

Crystal structure of Mycobacterium tuberculosis LpqY in complex with trehalose analogue YB-03

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x TY6- GLC: alpha-D-glucopyranose-(1-1)-(2~{S},3~{R},4~{S},5~{S},6~{S})-6-[(2-azanylhydrazinyl)methyl]oxane-2,3,4,5-tetrol(Non-covalent)

TY6-GLC.1: 18 residues within 4Å: Chain A: P.40, T.42, D.43, R.71, P.73, Q.76, D.97, V.98, N.151, E.196, G.197, V.200, W.276, F.278, G.350, G.351, L.388, R.421 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.43, A:Q.76, A:N.151, A:D.97, A:N.151, A:W.276, A:G.351, A:R.421, A:R.421 Water bridges: A:Q.76

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

SO4.2: 4 residues within 4Å: Chain A: R.71, 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 SO4.3: 8 residues within 4Å: Chain A: Q.191, A.192, N.193, Q.194, G.195, E.196, G.197, L.198 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.191, A:N.193, A:N.193, A:G.195, A:G.197, A:L.198 Water bridges: A:Q.194, A:Q.194 SO4.4: 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 SO4.5: 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 SO4.6: 2 residues within 4Å: Chain A: H.220, Q.458 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.458, A:Q.458, A:Q.458, A:Q.458 Salt bridges: A:H.220 SO4.7: 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

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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