MolNFT v1 · #51868 · protein
The structure of clostridium perfringens nani sialidase and its catalytic intermediates
2VK5 · Exo-alpha-sialidase: “The structure of clostridium perfringens nani sialidase and its catalytic intermediates”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.62). MolNFT v1 #51868 on GenesisL1: 3D structure…
- PDB
- 2VK5
- Type
- protein
- Length
- 448 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-alpha-sialidase
- EC
- 3.2.1.18
- UniProt
- Q59310
- Ligands
- CA
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-alpha-sialidase (EC 3.2.1.18) | protein | 448 | 3% helix, 48% strand | Q59310 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.62 | 0.81 | 33 | empty |
| 2 | 266 | 0.62 | 0.80 | 30 | empty |
| 3 | 131 | 0.49 | 0.79 | 24 | empty |
| 4 | 65 | 0.29 | 0.74 | 16 | empty |
Compared structures
- 2VK5 · The structure of clostridium perfringens nani sialidase and its catalytic intermediates · 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 Q59310
- Elsewhere: RCSB PDB 2VK5 · PDBe 2VK5 · UniProt Q59310
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