SMTL ID : 6dxu.1

Crystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

3 x BCN: BICINE(Non-covalent)

BCN.1: 9 residues within 4Å: Chain A: R.523, G.561, D.562, W.563, D.603, N.604, P.605, K.766, Q.793 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.523, A:D.562, A:D.603, A:Q.793, A:Q.793 BCN.8: 8 residues within 4Å: Chain D: R.523, D.562, W.563, D.603, N.604, P.605, K.766, Q.793 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.523, D:R.523, D:D.603, D:K.766, D:K.766, D:Q.793 BCN.9: 6 residues within 4Å: Chain D: V.251, F.252, M.270, K.271, I.272, K.273 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.271, D:K.273

8 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: D.78, A.79, D.81, V.84, Y.608 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.78 Water bridges: A:Y.86 NA.3: 4 residues within 4Å: Chain A: D.173, M.176, P.178, S.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.173 Water bridges: A:D.180 NA.4: 5 residues within 4Å: Chain B: D.78, A.79, D.81, V.84, Y.608 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.78 Water bridges: B:Y.86 NA.5: 4 residues within 4Å: Chain B: D.173, M.176, P.178, S.179 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.178 NA.6: 5 residues within 4Å: Chain C: D.78, A.79, D.81, V.84, Y.608 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.84 NA.7: 4 residues within 4Å: Chain C: D.173, M.176, P.178, S.179 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.178 Water bridges: C:D.436 NA.10: 5 residues within 4Å: Chain D: D.78, A.79, D.81, V.84, Y.608 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.84 Water bridges: D:Y.86 NA.11: 4 residues within 4Å: Chain D: D.173, M.176, P.178, S.179 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Little, M.S. et al., Active site flexibility revealed in crystal structures of Parabacteroides merdae beta-glucuronidase from the human gut microbiome. Protein Sci. (2018)

Release Date

2019-02-27

Peptides

Glycosyl hydrolase family 2, TIM barrel domain protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

Glycosyl hydrolase family 2, TIM barrel domain protein

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