SMTL ID : 3bvv.1

Golgi mannosidase II D204A catalytic nucleophile mutant complex with METHYL ALPHA-D-MANNOPYRANOSYL-(1->3)-[6-THIO-ALPHA-D-MANNOPYRANOSYL-(1->6)]-BETA-D-MANNOPYRANOSIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x YZ0- MAN- Z4Y: alpha-D-mannopyranose-(1-3)-[6-thio-alpha-D-mannopyranose-(1-6)]methyl beta-D-mannopyranoside(Non-functional Binders)

YZ0-MAN-Z4Y.1: 19 residues within 4Å: Chain A: H.90, D.92, W.95, A.204, F.206, R.228, Y.269, R.289, L.295, D.340, D.341, R.343, W.415, H.471, D.472, Y.727, R.876, G.877 Ligands: ZN.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.92, A:R.228, A:Y.269, A:Y.269, A:D.472, A:Y.727, A:R.876, A:R.343, A:R.343 Water bridges: A:R.228, A:R.228, A:R.228, A:D.341, A:R.289

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: R.893, S.924 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.924 Water bridges: A:R.770, A:R.893, A:R.893, A:R.893 Salt bridges: A:R.893

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.90, D.92, A.204, H.471, D.472 Ligands: YZ0-MAN-Z4Y.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 MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 5 residues within 4Å: Chain A: K.63, Q.64, Y.267, H.273, P.279 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.63, A:Y.267, A:Y.267 Water bridges: A:Q.64

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

MPD.5: 8 residues within 4Å: Chain A: Y.435, Q.491, L.494, K.495, Q.498, L.526, D.528, W.531 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.435, A:D.528 MPD.6: 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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