SMTL ID : 5oar.1

Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

2 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 B: N.252, F.261, R.267, Y.269 Chain C: F.70 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.269 NAG-NAG-BMA.3: 8 residues within 4Å: Chain A: F.70, P.71 Chain D: N.252, T.258, F.261, R.267, T.268, Y.269 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.261

1 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: 3 residues within 4Å: Chain B: L.301, N.305, N.327 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.305

6 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.4: 4 residues within 4Å: Chain A: G.2, T.60, E.61, A.62 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.484, A:T.60 MAN.5: 5 residues within 4Å: Chain A: S.65, S.66, F.67 Chain D: D.191 Ligands: MAN.6 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.190 MAN.6: 5 residues within 4Å: Chain A: S.66, F.67, E.68, P.69 Ligands: MAN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.67 MAN.16: 3 residues within 4Å: Chain C: T.60, E.61, A.62 2 PLIP interactions: 2 interactions with chain C Water bridges: C:T.60, C:T.60 MAN.17: 5 residues within 4Å: Chain B: D.191 Chain C: S.65, S.66, F.67 Ligands: MAN.18 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.190 MAN.18: 4 residues within 4Å: Chain C: S.66, E.68, P.69 Ligands: MAN.17 No protein-ligand interaction detected (PLIP)

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

NAG.7: 5 residues within 4Å: Chain B: L.322, L.398, N.399 Chain D: M.362, A.363 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:A.363, B:L.322 NAG.19: 2 residues within 4Å: Chain B: M.362 Chain D: N.399 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.399 Hydrophobic interactions: B:M.362

2 x NGT: 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL(Non-covalent)

NGT.8: 12 residues within 4Å: Chain B: R.92, H.174, E.206, D.244, E.245, W.296, W.318, Y.344, D.346, W.381, W.416, E.418 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:D.244, B:W.296, B:W.318, B:W.416 Hydrogen bonds: B:R.92, B:R.92, B:H.174, B:D.346 NGT.21: 12 residues within 4Å: Chain D: R.92, H.174, E.206, D.244, E.245, W.296, W.318, Y.344, D.346, W.381, W.416, E.418 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.296, D:W.318, D:W.416 Hydrogen bonds: D:R.92, D:R.92, D:H.174, D:D.244, D:D.346

11 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 2 residues within 4Å: Chain B: D.446, A.447 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: R.10 Chain B: K.76, S.78 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: R.331 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.358, G.379 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: D.18 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: R.267 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: N.371, F.372, N.377 Ligand excluded by PLIP CL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain D: R.358, G.379, W.381 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain D: R.267 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain D: N.371, F.372, N.377 Ligand excluded by PLIP

1 x TBR: HEXATANTALUM DODECABROMIDE(Non-covalent)

TBR.20: 4 residues within 4Å: Chain D: N.217, K.218, Y.220, E.221 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skerlova, J. et al., Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide. FEBS J. (2018)

Release Date

2017-12-27

Peptides

Beta-hexosaminidase: AC
Beta-hexosaminidase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Beta-hexosaminidase

Beta-hexosaminidase