SMTL ID : 8frd.1 (1 other biounit)

Mouse acidic mammalian chitinase, catalytic domain in complex with N,N'-diacetylchitobiose at pH 5.25

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 18 residues within 4Å: Chain A: N.30, W.31, F.58, I.69, G.98, W.99, N.100, Y.267, H.269, T.295, Q.297, F.300, W.360, L.364 Chain B: S.88 Ligands: NAG-NAG.2, NAG-NAG.3, NAG-NAG.3 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.88, A:N.100 Hydrophobic interactions: A:W.31 Water bridges: A:Q.297, A:Q.297 NAG-NAG.2: 18 residues within 4Å: Chain A: W.99, E.140, Y.141, A.185, G.186, G.187, I.188, N.190, M.210, Y.212, D.213, L.214, W.218, L.241, H.269 Ligands: NAG-NAG.1, NAG-NAG.3, NAG-NAG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.140, A:D.213, A:D.213 Water bridges: A:G.186, A:H.269, A:Q.297 NAG-NAG.3: 23 residues within 4Å: Chain A: Y.27, W.31, F.58, G.98, W.99, N.100, D.138, E.140, Y.141, A.183, A.185, G.186, M.210, Y.212, D.213, W.218, Y.267, H.269, M.358, W.360 Ligands: NAG-NAG.1, NAG-NAG.2, NAG-NAG.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.183, A:W.360 Hydrogen bonds: A:W.99, A:Y.212 Water bridges: A:D.213, A:H.269 NAG-NAG.4: 19 residues within 4Å: Chain B: Y.27, W.31, F.58, G.98, W.99, N.100, D.138, E.140, A.183, M.210, Y.212, D.213, Y.267, Q.297, F.300, M.358, W.360, L.364 Ligands: NAG-NAG.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.267, B:F.300 Hydrogen bonds: B:W.99, B:N.100, B:N.100, B:N.100, B:Q.297, B:W.360 Water bridges: B:F.101 NAG-NAG.5: 17 residues within 4Å: Chain B: W.99, E.140, Y.141, A.185, G.186, G.187, I.188, N.190, M.210, Y.212, D.213, L.214, W.218, L.241, H.269 Ligands: NAG-NAG.4, NAG-NAG.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.140, B:Y.141, B:D.213 Water bridges: B:G.186, B:H.269

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: S.277, D.278, N.279 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.277, H2O.2, H2O.7, H2O.10 MG.7: 2 residues within 4Å: Chain B: S.277, D.278 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.277, H2O.15, H2O.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz, R.E. et al., Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. Biorxiv (2024)

Release Date

2023-03-15

Peptides

Acidic mammalian chitinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acidic mammalian chitinase

Related Entries With Identical Sequence