SMTL ID : 1qwn.1

GOLGI ALPHA-MANNOSIDASE II Covalent Intermediate Complex with 5-fluoro-gulosyl-fluoride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.194 Water bridges: A:K.154, A:N.194

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.90, D.92, D.204, H.471 Ligands: GUL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.90, A:D.92, A:D.204, A:H.471

1 x GUL: (2R,3S,4R,5S)-2,6-difluoro-2-(hydroxymethyl)oxane-3,4,5-triol(Post Translational Modification)

GUL.3: 15 residues within 4Å: Chain A: H.90, D.92, W.95, D.204, F.206, R.228, Y.269, D.341, W.415, H.471, D.472, Y.727, R.876 Ligands: ZN.2, TRS.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.228, A:Y.269, A:Y.727, A:R.876

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 5 residues within 4Å: Chain A: R.228, Y.269, D.340, D.341 Ligands: GUL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.228, A:D.340 Water bridges: A:R.228, A:D.270, A:D.341

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

MPD.5: 6 residues within 4Å: Chain A: K.63, Q.64, Y.267, H.273, P.279, R.410 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.63, A:K.63, A:Y.267 Water bridges: A:Q.64, A:Q.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Numao, S. et al., Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates. J.Biol.Chem. (2003)

Release Date

2003-10-07

Peptides

Alpha-mannosidase II: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-mannosidase II

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