SMTL ID : 2ow6.1

Golgi alpha-mannosidase II complex with (1r,5s,6s,7r,8s)-1-thioniabicyclo[4.3.0]nonan-5,7,8-triol chloride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.19 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:N.194

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

PO4.2: 3 residues within 4Å: Chain A: E.566, R.893, S.924 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.924 Water bridges: A:E.566, A:Q.567, A:A.773, A:R.893, A:R.893 Salt bridges: A:R.893 PO4.3: 2 residues within 4Å: Chain A: F.137, L.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.103, A:Y.103 Water bridges: A:S.112, A:G.142

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.90, D.92, D.204, H.471 Ligands: NK1.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.90, A:D.92, A:D.204, A:H.471

1 x NK1: (1R,5S,6S,7R,8S)-1-THIONIABICYCLO[4.3.0]NONAN-5,7,8-TRIOL(Non-covalent)

NK1.5: 13 residues within 4Å: Chain A: 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.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.204, A:Y.727, A:Y.727 Water bridges: A:R.228 Salt bridges: A:D.92, A:D.204, A:D.341 pi-Cation interactions: A:W.95

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

MRD.6: 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:K.63, A:Q.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, N.S. et al., Binding of sulfonium-ion analogues of di-epi-swainsonine and 8-epi-lentiginosine to Drosophila Golgi alpha-mannosidase II: The role of water in inhibitor binding. Proteins (2008)

Release Date

2008-01-08

Peptides

Alpha-mannosidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-mannosidase 2

Related Entries With Identical Sequence