Research workbench
Golgi mannosidase II D204A catalytic nucleophile mutant complex with methyl (alpha-D-mannopyranosyl)-(1->3)-S-alpha-D-mannopyranoside
Analyse Golgi mannosidase II D204A catalytic nucleophile mutant complex with methyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BVT
- 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
- Z4R, MAN, NAG, ZN, PO4
- Pockets
- 15 · best druggability 0.79
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
- Z4R · methyl 3-thio-alpha-D-mannopyranoside · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- 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 · 2 copies · 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
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.79 | 0.98 | 28 | empty |
| 2 | 179 | 0.78 | 0.94 | 30 | empty |
| 3 | 674 | 0.73 | 0.79 | 94 | PO4 |
| 4 | 257 | 0.63 | 0.81 | 33 | empty |
| 5 | 180 | 0.53 | 0.79 | 23 | Z4R, MAN, ZN |
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3BVT · GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl… · 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 3BVT · PDBe 3BVT · UniProt Q24451
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