MolNFT v1 · #51869 · protein
The structure of clostridium perfringens nani sialidase and its catalytic intermediates
2VK6 · Exo-alpha-sialidase: “The structure of clostridium perfringens nani sialidase and its catalytic intermediates”. X-ray diffraction, 3 ligands (DAN, MG, CA), 4 pockets (best druggability 0.64). MolNFT v1 #51869 on GenesisL1: 3D…
- PDB
- 2VK6
- 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
- DAN, MG, CA
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-alpha-sialidase (EC 3.2.1.18) | protein | 448 | 2% helix, 48% strand | Q59310 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.64 | 0.81 | 36 | empty |
| 2 | 237 | 0.62 | 0.81 | 31 | empty |
| 3 | 126 | 0.52 | 0.81 | 22 | DAN |
| 4 | 65 | 0.32 | 0.76 | 17 | empty |
Compared structures
- 2VK6 · 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 2VK6 · PDBe 2VK6 · UniProt Q59310
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