Research workbench
Golgi alpha-mannosidase II complex with benzyl-mannostatin a
Analyse Golgi alpha-mannosidase II complex with benzyl-mannostatin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F7P
- Type
- protein
- Length
- 1,014 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-mannosidase II
- EC
- 3.2.1.114
- UniProt
- Q24451
- Ligands
- 2SK, 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 II (EC 3.2.1.114) | protein | 1014 | 24% helix, 30% strand | Q24451 |
Ligands and binding sites
- 2SK · (1R,2R,3R,4S,5R)-4-(benzylamino)-5-(methylthio)cyclopentane-1,2,3-triol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · 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 | 140 | 0.80 | 0.97 | 34 | empty |
| 2 | 256 | 0.74 | 0.88 | 39 | empty |
| 3 | 616 | 0.71 | 0.79 | 89 | empty |
| 4 | 263 | 0.63 | 0.81 | 34 | empty |
| 5 | 237 | 0.53 | 0.76 | 35 | 2SK |
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
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 2F7P · PDBe 2F7P · UniProt Q24451
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.