Research workbench
Golgi mannosidase II D204A catalytic nucleophile mutant with an empty active site
Analyse Golgi mannosidase II D204A catalytic nucleophile mutant with an empty active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BUD
- 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
- NAG, ZN, PO4
- 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · 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 | 130 | 0.80 | 0.98 | 32 | empty |
| 2 | 248 | 0.74 | 0.88 | 37 | empty |
| 3 | 676 | 0.72 | 0.79 | 95 | PO4 |
| 4 | 252 | 0.63 | 0.82 | 33 | empty |
| 5 | 218 | 0.54 | 0.78 | 31 | ZN, MPD |
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3BUD · Golgi mannosidase II D204A catalytic nucleophile mutant with an empty active site · the same entry in another collection · chain A against A, TM-score 1.00
- Q24451 · AlphaFold monomer V2.0 prediction for alpha-mannosidase 2 (Q24451) · a predicted model of the same protein · 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 3BUD · PDBe 3BUD · UniProt Q24451
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