SMTL ID : 3bvw.1

GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl (2-deoxy-2-acetamido-beta-D-glucopyranosyl)-(1->2)-ALPHA-D-mannopyranosyl- (1->3)-[ALPHA-D-mannopyranosyl-(1->6)-6-thio-alpha-D-mannopyranosyl- (1->6)]-BETA-D-mannopyranoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x YZ0- MAN- NAG- Z4Y- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-6-thio-alpha-D-mannopyranose-(1-6)]methyl beta-D-mannopyranoside(Non-covalent)

YZ0-MAN-NAG-Z4Y-MAN.1: 24 residues within 4Å: Chain A: K.63, Q.64, H.90, D.92, W.95, A.204, F.206, R.228, Y.267, Y.269, H.273, P.279, P.298, W.299, D.341, R.410, W.415, H.471, D.472, Y.727, E.875, R.876, G.877 Ligands: ZN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.92, A:R.228, A:R.228, A:Y.269, A:Y.269, A:D.472, A:Y.727, A:H.273, A:Y.267 Hydrophobic interactions: A:P.298, A:W.299 Water bridges: A:K.63, A:K.63, A:Q.64, A:Y.267, A:Y.267, A:R.410, A:S.268, A:D.270

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.90, D.92, A.204, H.471, D.472 Ligands: YZ0-MAN-NAG-Z4Y-MAN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.90, A:D.92, A:D.92, A:H.471

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

MPD.3: 4 residues within 4Å: Chain A: R.457, K.495, A.496, M.499 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.457 Hydrogen bonds: A:K.495, A:K.495 Water bridges: A:R.457, A:A.496

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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