Research workbench
Golgi alpha-mannosidase II complex with benzyl-aminocyclopentitetrol
Analyse Golgi alpha-mannosidase II complex with benzyl-aminocyclopentitetrol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F7R
- 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
- Ligands
- SK3, NAG, ZN
- Pockets
- 11 · 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 | — |
Ligands and binding sites
- SK3 · (1R,2R,3S,4S,5R)-5-(benzylamino)cyclopentane-1,2,3,4-tetrol · 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.80 | 0.98 | 29 | empty |
| 2 | 291 | 0.73 | 0.87 | 51 | empty |
| 3 | 618 | 0.72 | 0.79 | 92 | empty |
| 4 | 236 | 0.62 | 0.81 | 31 | empty |
| 5 | 248 | 0.54 | 0.77 | 34 | SK3 |
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2F7R · Golgi alpha-mannosidase II complex with benzyl-aminocyclopentitetrol · 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
- Elsewhere: RCSB PDB 2F7R · PDBe 2F7R
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