SMTL ID : 9ftq.1

Drosophila golgi alpha-mannosidase II (dGMII) in complex with swainsonine-configured alkyl indolizidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 1 residues within 4Å: Chain A: N.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.182 PEG.2: 8 residues within 4Å: Chain A: S.522, R.528, D.558, Y.560, V.583, W.584, R.605, R.765 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.522, A:R.528, A:Y.560, A:W.584, A:W.584

1 x 01: swainsonine-configured alkyl indolizidine

01.3: 13 residues within 4Å: Chain A: H.78, D.80, W.83, D.192, F.194, R.216, Y.257, W.403, H.459, D.460, T.465, Y.715 Ligands: ZN.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.194, A:W.403, A:W.403, A:Y.715 Hydrogen bonds: A:D.460, A:T.465 Salt bridges: A:D.80, A:D.192, A:D.329, A:D.460 pi-Cation interactions: A:W.83

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.78, D.80, D.192, H.459 Ligands: 01.3 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

Koemans, T. et al., Structure-guided design of C3-branched swainsonine as potent and selective human Golgi alpha-mannosidase (GMII) inhibitor. Chem.Commun.(Camb.) (2024)

Release Date

2024-10-09

Peptides

Alpha-mannosidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-mannosidase 2

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