Research workbench
The structure of clostridium perfringens nani sialidase and its catalytic intermediates
Analyse The structure of clostridium perfringens nani sialidase and its catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VK7
- Type
- protein
- Length
- 896 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-alpha-sialidase
- EC
- 3.2.1.18
- UniProt
- Q59310
- Ligands
- FSI, CA
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exo-alpha-sialidase (EC 3.2.1.18) | protein | 448 | 2% helix, 49% strand | Q59310 |
Ligands and binding sites
- FSI · 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.76 | 0.83 | 55 | FSI |
| 2 | 406 | 0.73 | 0.83 | 50 | empty |
| 3 | 311 | 0.64 | 0.80 | 37 | empty |
| 4 | 245 | 0.63 | 0.82 | 25 | empty |
| 5 | 324 | 0.61 | 0.79 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 543 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2VK7 · 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 2VK7 · PDBe 2VK7 · UniProt Q59310
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.