SMTL ID : 7vi7.2 (1 other biounit)

Crystal structure of GH3 beta-N-acetylhexosaminidase Amuc_2109 from Akkermansia muciniphila in complex with GlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.1: 12 residues within 4Å: Chain A: I.30, F.32, D.62, F.113, R.132, K.162, H.163, M.167, M.207, D.246, D.247, L.275 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.132, A:R.132, A:K.162, A:H.163, A:D.246, A:D.246, A:D.247 Water bridges: A:D.247

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.173, F.176 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.173, A:F.176, H2O.3, H2O.5, H2O.7, H2O.7 MG.3: 2 residues within 4Å: Chain A: D.37, S.73 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.37, A:S.73, H2O.2, H2O.6, H2O.7 MG.4: 5 residues within 4Å: Chain A: R.50, C.53, L.54, H.55, P.57 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.50, A:C.53, A:H.55, H2O.1, H2O.8 MG.5: 2 residues within 4Å: Chain A: C.120, C.133 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.120, A:C.133, H2O.7

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

CL.6: 3 residues within 4Å: Chain A: D.184, E.185, R.186 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.67, S.80, R.86, G.131 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: G.14, A.15, E.16, E.17 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: G.88, R.144 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: G.238, F.239, R.240 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qian, K. et al., Functional and structural characterization of a GH3 beta-N-acetylhexosaminidase from Akkermansia muciniphila involved in mucin degradation. Biochem.Biophys.Res.Commun. (2022)

Release Date

2021-12-22

Peptides

Beta-N-acetylhexosaminidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-N-acetylhexosaminidase

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