SMTL ID : 6rs0.1

GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3S,4R,5R)-1-(2-(Benzyloxy)ethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.78, D.80, D.192, H.459 Ligands: KGB.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:D.80, A:D.192, A:H.459

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

EDO.2: 7 residues within 4Å: Chain A: R.164, N.165, L.168, M.421, V.424, R.425, V.949 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.165 Water bridges: A:R.164, A:E.428, A:R.951 EDO.3: 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

1 x KGB: (2~{S},3~{S},4~{R})-2-(hydroxymethyl)-1-(2-phenylmethoxyethyl)piperidine-3,4,5-triol(Non-covalent)

KGB.4: 13 residues within 4Å: Chain A: H.78, D.80, W.83, D.192, F.194, R.216, Y.257, D.329, H.459, D.460, Y.715, R.864 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.216, A:Y.257, A:Y.715 Salt bridges: A:D.80, A:D.192, A:D.329

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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