SMTL ID : 6ddt.1

mouse beta-mannosidase (MANBA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 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 Hydrophobic interactions: A:L.99 Hydrogen bonds: A:T.104, A:N.102

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 A: Q.246, N.291, K.309 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 3 residues within 4Å: Chain A: N.792, T.794, E.809 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: 6 residues within 4Å: Chain A: L.64, D.65, N.66, R.134, S.135, Q.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.65, A:N.66, A:Q.138 Water bridges: A:L.64 NAG.6: 2 residues within 4Å: Chain A: E.277, N.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.286 Water bridges: A:T.278 NAG.7: 3 residues within 4Å: Chain A: N.22, N.24, S.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.24, A:S.26

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

EDO.8: 11 residues within 4Å: Chain A: M.111, K.172, A.173, C.175, S.176, P.348, D.350, S.351, Q.353, I.383, I.651 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.353 Water bridges: A:D.93, A:K.172, A:S.351, A:Q.353 EDO.9: 10 residues within 4Å: Chain A: A.349, R.360, L.364, N.649, D.650, L.660, E.661, Y.662, G.663, G.664 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.349, A:N.649, A:D.650, A:L.660 EDO.10: 7 residues within 4Å: Chain A: L.14, S.15, G.16, S.17, W.18, T.71, F.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.17 EDO.11: 7 residues within 4Å: Chain A: W.179, D.180, W.181, Y.523, Y.525, W.646, W.657 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.179, A:W.181

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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