Research workbench
Golgi alpha-mannosidase II in complex with 5-substituted swainsonine analog: (5R)-5-[2'-oxo-2'-(PHENYL)ETHYL]-swainsonine
Analyse Golgi alpha-mannosidase II in complex with 5-substituted swainsonine analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EJP
- Type
- protein
- Length
- 1,016 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-mannosidase 2
- EC
- 3.2.1.114
- UniProt
- Q24451
- Ligands
- HN2, NAG, ZN
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-mannosidase 2 (EC 3.2.1.114) | protein | 1016 | 24% helix, 30% strand | Q24451 |
Ligands and binding sites
- HN2 · 1-phenyl-2-[(1S,2R,5R,8R,8aR)-1,2,8-trihydroxyoctahydroindolizin-5-yl]ethanone · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.80 | 0.98 | 31 | empty |
| 2 | 261 | 0.75 | 0.89 | 50 | empty |
| 3 | 640 | 0.72 | 0.80 | 94 | empty |
| 4 | 280 | 0.63 | 0.81 | 33 | empty |
| 5 | 221 | 0.52 | 0.77 | 28 | HN2 |
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3EJP · Golgi alpha-Mannosidase II in complex with 5-substituted swainsonine analog… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q24451
- Elsewhere: RCSB PDB 3EJP · PDBe 3EJP · UniProt Q24451
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