SMTL ID : 4zmh.1

Crystal structure of a five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: F.176, N.178, Y.390, H.392, Y.395, N.432 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.178, A:Y.390, A:N.432 Water bridges: A:N.178, A:H.392, A:H.392, A:V.396 Salt bridges: A:H.392 PO4.2: 3 residues within 4Å: Chain A: N.89, K.101, H.163 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.92, A:K.101, A:K.101 Salt bridges: A:K.101, A:H.163 PO4.3: 4 residues within 4Å: Chain A: H.57, S.58, Q.59, D.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.58, A:Q.59 Salt bridges: A:H.57 PO4.8: 6 residues within 4Å: Chain B: F.176, N.178, Y.390, H.392, Y.395, N.432 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.178, B:N.178, B:Y.390, B:Y.390, B:N.432 Salt bridges: B:H.392

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

NA.4: 4 residues within 4Å: Chain A: D.394, R.403, D.435, Q.612 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.394 NA.9: 4 residues within 4Å: Chain B: R.403, W.404, D.435, Q.612 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.394

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: K.344, R.373, W.845, H.875 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.373, A:R.373 Water bridges: A:K.344, A:D.348 GOL.6: 3 residues within 4Å: Chain A: G.397, G.398, W.620 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: H.247, R.295, Y.343, K.344, N.368, Y.395 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.343, A:Y.343, A:N.368, A:Y.395 Salt bridges: A:K.344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Biochemical and Structural Characterization of a Five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T. J.Biol.Chem. (2016)

Release Date

2016-05-04

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uncharacterized protein