SMTL ID : 3bui.1

Golgi mannosidase II D204A catalytic nucleophile mutant complex with Tris

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.90, D.92, A.204, H.471, D.472 Ligands: TRS.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:D.92, A:H.471

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

TRS.2: 10 residues within 4Å: Chain A: H.90, D.92, W.95, F.206, R.228, Y.269, D.341, H.471, D.472 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.269, A:Y.269 Water bridges: A:R.228, A:R.228, A:R.228

4 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:Q.64 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:Y.435, A:L.494 Hydrogen bonds: A:L.526 Water bridges: A:L.526, A:D.528 MPD.5: 5 residues within 4Å: Chain A: Q.97, Y.102, D.106, D.341, F.342 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.102 Hydrogen bonds: A:D.106, A:D.341 Water bridges: A:Q.97 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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