SMTL ID : 6rqz.1

GOLGI ALPHA-MANNOSIDASE II complex with Manno-epi-cyclophellitol aziridine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

8 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: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: 6 residues within 4Å: Chain A: L.556, V.557, D.558, R.605, E.741, R.758 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.605 Water bridges: A:D.558, A:R.765 EDO.4: 3 residues within 4Å: Chain A: Y.494, Y.511, E.924 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.494 Water bridges: A:Y.494 EDO.5: 6 residues within 4Å: Chain A: R.216, Y.255, D.397, W.403, R.864 Ligands: KGH.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.216, A:R.216, A:Y.255 Water bridges: A:D.192 EDO.6: 4 residues within 4Å: Chain A: L.283, D.328, D.329, R.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.329, A:R.331 Water bridges: A:R.277 EDO.7: 4 residues within 4Å: Chain A: R.445, K.483, A.484, M.487 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.445 Water bridges: A:Q.448 EDO.8: 5 residues within 4Å: Chain A: S.540, K.541, H.542, F.922, N.925 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.540, A:H.542 Water bridges: A:K.541

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.9: 6 residues within 4Å: Chain A: S.522, R.528, D.558, Y.560, R.605, R.765 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.522 Water bridges: A:S.522, A:R.605, A:R.605, A:R.765, A:R.765, A:R.765 Salt bridges: A:R.528, A:R.605, A:R.765

1 x KGH: (1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-5-azanyl-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol(Covalent)

KGH.10: 15 residues within 4Å: Chain A: H.78, D.80, W.83, D.192, F.194, R.216, Y.257, D.329, W.403, H.459, D.460, Y.715, R.864 Ligands: EDO.5, ZN.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.83, A:D.192 Hydrogen bonds: A:R.216

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 6 residues within 4Å: Chain A: H.78, D.80, D.192, H.459, D.460 Ligands: KGH.10 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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