SMTL ID : 6rpc.1

GOLGI ALPHA-MANNOSIDASE II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: R.164, N.165, L.168, M.421, V.424, R.425, V.949 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.165 Water bridges: A:E.428, A:E.428 EDO.2: 5 residues within 4Å: Chain A: K.51, Y.255, H.261, P.267, W.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.51 Water bridges: A:Q.52 EDO.3: 7 residues within 4Å: Chain A: L.556, V.557, D.558, R.605, E.741, R.758 Ligands: SIN.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.605 Water bridges: A:D.558, A:R.758 EDO.4: 1 residues within 4Å: Chain A: E.924 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: V.31, L.36, E.224, Q.228, Q.230 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.224, A:E.224, A:Q.230 Water bridges: A:D.30, A:R.39, A:R.39 EDO.7: 6 residues within 4Å: Chain A: D.192, F.194, R.216, W.403, Y.715, R.864 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.192, A:R.216, A:R.864 Water bridges: A:R.216 EDO.8: 6 residues within 4Å: Chain A: G.523, W.586, V.752, Q.754, L.767, L.877 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.754 Water bridges: A:G.523

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.5: 7 residues within 4Å: Chain A: S.522, R.528, D.558, Y.560, R.605, R.765 Ligands: EDO.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.522, A:D.558 Water bridges: A:S.522, A:R.605, A:R.605, A:Q.754 Salt bridges: A:R.528, A:R.605, A:R.765

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain A: H.78, D.80, D.192, H.459 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.78, A:D.80, A:D.192, A:H.459, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Armstrong, Z. et al., Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. J.Am.Chem.Soc. (2020)

Release Date

2020-07-08

Peptides

Alpha-mannosidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-mannosidase 2

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