SMTL ID : 3bvt.1

GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl (alpha-D-mannopyranosyl)-(1->3)-S-alpha-D-mannopyranoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x Z4R- MAN: alpha-D-mannopyranose-(1-3)-methyl 3-thio-alpha-D-mannopyranoside(Non-covalent)

Z4R-MAN.1: 17 residues within 4Å: Chain A: H.90, D.92, W.95, A.204, F.206, R.228, S.268, Y.269, D.270, D.341, W.415, H.471, D.472, Y.727, E.875, R.876 Ligands: ZN.4 6 PLIP interactions: 6 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.228, A:S.268, A:D.270 Water bridges: A:R.228, A:S.268, A:Y.269, A:D.341

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

NAG.2: 1 residues within 4Å: Chain A: N.194 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.194

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

PO4.3: 2 residues within 4Å: Chain A: R.893, S.924 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.924 Water bridges: A:R.770, A:R.893, A:R.893, A:R.893, A:R.893 Salt bridges: A:R.893

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: H.90, D.92, A.204, H.471, D.472 Ligands: Z4R-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 MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 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.6: 7 residues within 4Å: Chain A: Y.435, Q.491, L.494, K.495, Q.498, L.526, W.531 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.494 Water bridges: A:Q.498, A:D.528, A:W.531 MPD.7: 4 residues within 4Å: Chain A: Y.102, D.106, D.341, F.342 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.102 Hydrogen bonds: A:D.106, A:D.341 Water bridges: A:Q.97, A:Q.97

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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