SMTL ID : 3bub.1

Golgi alpha-mannosidase II with an empty active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: K.154, N.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.194

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.90, D.92, D.204, H.471 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.90, A:D.92, A:D.204, A:H.471, H2O.1

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: K.63, Q.64, Y.267, H.273, P.279, R.410 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.63, A:Y.267, A:Y.267 Water bridges: A:V.61 MPD.4: 8 residues within 4Å: Chain A: Y.435, Q.491, L.494, K.495, Q.498, L.526, D.528, W.531 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.528 Hydrogen bonds: A:L.526 Water bridges: A:Q.498, A:Q.498, A:Q.498 MPD.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, W. et al., Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant. J.Am.Chem.Soc. (2008)

Release Date

2008-07-01

Peptides

Alpha-mannosidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-mannosidase 2

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