SMTL ID : 6rry.1

GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymethyl)-1,2,3,6-tetrahydro-3-pyridinol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

3 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 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: 4 residues within 4Å: Chain A: K.51, Y.255, H.261, W.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.51, A:Q.52 Water bridges: A:W.287 EDO.5: 6 residues within 4Å: Chain A: L.556, V.557, D.558, R.605, E.741, R.758 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.605, A:E.741 Water bridges: A:D.558, A:R.758

1 x KGE: (2~{S},3~{R})-2-(hydroxymethyl)-1,2,3,6-tetrahydropyridin-3-ol(Non-covalent)

KGE.2: 11 residues within 4Å: Chain A: D.80, W.83, D.192, F.194, R.216, Y.257, H.459, D.460, Y.715, R.864 Ligands: ZN.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.194, A:Y.715 Hydrogen bonds: A:Y.257, A:Y.257, A:D.460, A:Y.715

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.4: 6 residues within 4Å: Chain A: S.522, R.528, Y.560, R.605, Q.754, R.765 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.522, A:Y.560, A:Q.754 Water bridges: A:R.605, A:R.605, A:S.743 Salt bridges: A:R.528, A:R.605, A:R.765

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.78, D.80, D.192, H.459 Ligands: KGE.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:D.80, A:D.192, A:H.459

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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