SMTL ID : 4xwh.1

Crystal structure of the human N-acetyl-alpha-glucosaminidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: N.249, S.251, Y.252, P.628, E.629 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 1 residues within 4Å: Chain A: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: E.398, L.475, R.476, N.480 No protein-ligand interaction detected (PLIP)

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 3 residues within 4Å: Chain A: N.238, A.259, P.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.238 NAG.5: 2 residues within 4Å: Chain A: N.503, S.505 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.503, A:S.505 NAG.6: 2 residues within 4Å: Chain A: N.509, S.511 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.511

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain A: N.111, V.112, C.113, N.292, E.293, Q.327, W.329, L.384, E.423 Ligands: XYL.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.111, A:N.292, A:E.293, A:Q.327, A:Q.327 Water bridges: A:E.293 GOL.8: 4 residues within 4Å: Chain A: W.124, R.205, D.208, Q.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.205, A:R.205 GOL.9: 5 residues within 4Å: Chain A: W.245, G.246, E.293, H.333, I.632 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.246, A:H.333

2 x XYL: Xylitol(Non-covalent)

XYL.10: 10 residues within 4Å: Chain A: Y.42, A.64, H.67, R.68, R.71, L.136, N.137, A.436, E.437, W.440 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.42, A:A.64, A:H.67, A:R.68, A:R.71, A:N.137, A:W.440 XYL.11: 11 residues within 4Å: Chain A: C.113, Y.117, W.178, W.245, E.293, W.329, E.423, W.626, I.632, Y.635 Ligands: GOL.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.117, A:Y.117, A:E.423, A:Y.635 Water bridges: A:W.178, A:N.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birrane, G. et al., Structural characterization of the alpha-N-acetylglucosaminidase, a key enzyme in the pathogenesis of Sanfilippo syndrome B. J.Struct.Biol. (2019)

Release Date

2016-02-03

Peptides

Alpha-N-acetylglucosaminidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-N-acetylglucosaminidase