SMTL ID : 6ddu.1

mouse beta-mannosidase bound to beta-D-mannose (MANBA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

monomer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 5 residues within 4Å: Chain A: E.97, L.99, N.102, V.103, T.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.104, A:T.104, A:T.104, A:N.102 NAG-FUC.3: 3 residues within 4Å: Chain A: N.792, T.794, E.809 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.809 Hydrogen bonds: A:T.794

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: 2 residues within 4Å: Chain A: Q.246, N.291 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 9 residues within 4Å: Chain A: T.497, N.498, P.512, Y.513, S.514, Y.517, G.518, D.519, I.520 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.497, A:P.512, A:S.514, A:Y.517, A:D.519

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

NAG.5: 5 residues within 4Å: Chain A: L.64, D.65, N.66, R.134, Q.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.65, A:N.66, A:Q.138 NAG.6: 2 residues within 4Å: Chain A: E.277, N.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.286 NAG.7: 2 residues within 4Å: Chain A: N.24, S.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.24

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.8: 14 residues within 4Å: Chain A: W.179, D.180, W.181, R.377, W.379, S.408, N.445, E.446, H.521, Y.523, E.543, W.646, W.657 Ligands: EDO.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.179, A:D.180, A:W.181, A:W.379, A:S.408, A:N.445, A:E.543, A:W.646 Salt bridges: A:H.521

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 5 residues within 4Å: Chain A: Q.161, W.179, D.180, S.408 Ligands: BMA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.161, A:D.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gytz, H. et al., The structure of mammalian beta-mannosidase provides insight into beta-mannosidosis and nystagmus. FEBS J. (2019)

Release Date

2019-01-09

Peptides

Beta-mannosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-mannosidase

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