SMTL ID : 4qhz.1

Crystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-tetramer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: F.44, D.169, I.192 Chain B: F.44, D.169, I.192 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.169, A:D.169 Water bridges: B:D.169, B:G.195, A:D.169, A:G.195 EDO.4: 6 residues within 4Å: Chain C: F.44, D.169, I.192 Chain D: F.44, D.169, I.192 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:D.169, D:G.195, C:D.169, C:G.195 EDO.6: 6 residues within 4Å: Chain B: L.205, F.213, P.214 Chain D: L.205, F.213, P.214 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: N.118, S.119, G.120, E.128, Q.130, Q.227 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.119, A:E.128, H2O.1 MG.3: 6 residues within 4Å: Chain B: N.118, S.119, E.128, Q.130, V.131, Q.227 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.119, B:E.128, H2O.11 MG.5: 5 residues within 4Å: Chain C: N.118, S.119, E.128, Q.130, Q.227 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.119, C:E.128, H2O.19 MG.7: 5 residues within 4Å: Chain D: N.118, S.119, E.128, Q.130, Q.227 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.119, D:E.128, H2O.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution. To be published

Release Date

2014-07-30

Peptides

putative glycosyl hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

putative glycosyl hydrolase