MolNFT v1 · #53564 · protein
Structure of the streptococcus pyogenes family GH38 alpha- mannosidase complexed with swainsonine
2WYI · Alpha-mannosidase: “Structure of the streptococcus pyogenes family GH38 alpha- mannosidase complexed with swainsonine”. X-ray diffraction, 2 ligands (SWA, ZN), 18 pockets (best druggability 0.81). MolNFT v1 #53564 on GenesisL1: 3D…
- PDB
- 2WYI
- Type
- protein
- Length
- 1,792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-mannosidase
- EC
- 3.2.1.24
- UniProt
- Q99YP5
- Ligands
- SWA, ZN
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-mannosidase (EC 3.2.1.24) | protein | 896 | 25% helix, 34% strand | Q99YP5 |
| B | Alpha-mannosidase (EC 3.2.1.24) | protein | 896 | 25% helix, 34% strand | Q99YP5 |
Ligands and binding sites
- SWA · 1S-8AB-octahydro-indolizidine-1A,2A,8B-triol · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.81 | 0.84 | 57 | empty |
| 2 | 1142 | 0.75 | 0.78 | 106 | PG0 |
| 3 | 180 | 0.67 | 0.86 | 20 | empty |
| 4 | 159 | 0.66 | 0.86 | 21 | empty |
| 5 | 414 | 0.65 | 0.78 | 42 | PG0 |
Interfaces
1 interface between chains.
- A–B · 3000 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2WYI · Structure of the Streptococcus pyogenes family GH38 alpha-mannosidase complexed with… · 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 Q99YP5
- Elsewhere: RCSB PDB 2WYI · PDBe 2WYI · UniProt Q99YP5
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