SMTL ID : 3ejt.1

Golgi alpha-Mannosidase II in complex with 5-substituted swainsonine analog:(5R)-5-[2'-(4-tert-butylphenyl)ethyl]-swainsonine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.154

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.90, D.92, D.204, H.471 Ligands: HN6.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.90, A:D.92, A:D.204, A:H.471

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 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

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 4 residues within 4Å: Chain A: W.445, H.446, F.946, L.1003 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.446

1 x HN6: (1S,2R,5R,8R,8aR)-5-[2-(4-tert-butylphenyl)ethyl]octahydroindolizine-1,2,8-triol(Non-covalent)

HN6.5: 16 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, E.875, R.876, G.877 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.206, A:W.415, A:Y.727 Hydrogen bonds: A:Y.269, A:D.472, A:Y.727 Salt bridges: A:D.92, A:D.204, A:D.341, A:D.472 pi-Cation interactions: A:W.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuntz, D.A. et al., Structural Investigation of the Binding of 5-Substituted Swainsonine Analogues to Golgi alpha-Mannosidase II. Chembiochem (2010)

Release Date

2009-10-13

Peptides

Alpha-mannosidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-mannosidase 2

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