SMTL ID : 7pr6.1

Crystal structure of E. coli beta-glucuronidase in complex with covalent inhibitor ME727

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

4 x 8I4: (2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid(Post Translational Modification)

8I4.1: 15 residues within 4Å: Chain A: D.165, H.298, H.332, I.365, N.414, E.415, N.468, Y.470, Y.474, E.506, W.551, F.556, R.564, N.568, K.570 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.506 Hydrogen bonds: A:D.165, A:H.332, A:N.414, A:E.415, A:N.468, A:W.551, A:N.568 Water bridges: A:D.165, A:E.415, A:Y.470 Salt bridges: A:R.564, A:K.570 8I4.2: 14 residues within 4Å: Chain B: D.165, H.298, H.332, N.414, E.415, N.468, Y.470, Y.474, E.506, W.551, F.556, R.564, N.568, K.570 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:E.506 Hydrogen bonds: B:D.165, B:D.165, B:H.332, B:N.414, B:E.415, B:N.468, B:W.551, B:N.568, B:N.568 Water bridges: B:H.332, B:E.415, B:Y.470 Salt bridges: B:R.564, B:K.570 8I4.3: 15 residues within 4Å: Chain C: D.165, H.298, H.332, I.365, N.414, E.415, N.468, Y.470, Y.474, E.506, W.551, F.556, R.564, N.568, K.570 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:E.506 Hydrogen bonds: C:D.165, C:D.165, C:H.332, C:N.414, C:E.415, C:N.468, C:W.551, C:N.568 Water bridges: C:D.165, C:E.415, C:Y.470 Salt bridges: C:R.564, C:K.570 8I4.4: 14 residues within 4Å: Chain D: D.165, H.298, H.332, N.414, E.415, N.468, Y.470, Y.474, E.506, W.551, F.556, R.564, N.568, K.570 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:E.506 Hydrogen bonds: D:D.165, D:H.332, D:N.414, D:E.415, D:N.468, D:W.551, D:N.568, D:N.568 Water bridges: D:H.332, D:E.415, D:E.415, D:Y.470 Salt bridges: D:R.564, D:K.570

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Boer, C. et al., Mechanism-based heparanase inhibitors reduce cancer metastasis in vivo. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-08-03

Peptides

Beta-glucuronidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
AAA

D
BBB

Beta-glucuronidase

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