SMTL ID : 2ow7.1

Golgi alpha-mannosidase II complex with (1R,6S,7R,8S)-1-thioniabicyclo[4.3.0]nonan-7,8-diol chloride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 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 Hydrogen bonds: A:N.194

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: T.542, I.543, I.544, K.553, I.933, F.934 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.541, A:T.542, A:I.544, A:F.934 Water bridges: A:T.542 Salt bridges: A:K.553 SO4.3: 4 residues within 4Å: Chain A: W.598, H.600, V.764, L.779 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.598 SO4.4: 5 residues within 4Å: Chain A: W.445, H.446, L.508, F.946, L.1003 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.446 Salt bridges: A:H.446 SO4.5: 7 residues within 4Å: Chain A: S.534, W.598, V.764, Q.766, R.777, L.779, L.889 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.534, A:R.777, A:L.779 Water bridges: A:S.757 SO4.6: 2 residues within 4Å: Chain A: S.1044, S.1045 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.1045

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: H.90, D.92, D.204, H.471 Ligands: NK2.9 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.8: 6 residues within 4Å: Chain A: K.63, Q.64, Y.267, H.273, P.279, R.410 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.63, A:K.63, A:Y.267

1 x NK2: (1R,6S,7R,8S)-1-THIONIABICYCLO[4.3.0]NONAN-7,8-DIOL(Non-covalent)

NK2.9: 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.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.206, A:W.415, A:Y.727, A:R.876 Hydrogen bonds: A:Y.727, A:Y.727 Salt bridges: A:D.92, A:D.204, A:D.341 pi-Cation interactions: A:W.95

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

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