MolNFT v1 · #40279 · protein
Clostridium botulinum neurotoxin serotype a light chain inhibited by L-arginine hydroxamate
2IMB · Botulinum neurotoxin a light-chain: “Clostridium botulinum neurotoxin serotype a light chain inhibited by L-arginine hydroxamate”. X-ray diffraction, 2 ligands (AHL, ZN), 11 pockets (best druggability 0.78). MolNFT v1 #40279 on…
- PDB
- 2IMB
- Type
- protein
- Length
- 795 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin a light-chain
- EC
- 3.4.24.69
- UniProt
- Q7B8V4
- Ligands
- AHL, ZN
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin a light-chain (EC 3.4.24.69) | protein | 393 | 32% helix, 18% strand | Q7B8V4 |
| B | Botulinum neurotoxin a light-chain (EC 3.4.24.69) | protein | 402 | 30% helix, 16% strand | Q7B8V4 |
Ligands and binding sites
- AHL · N-hydroxy-L-argininamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.78 | 0.79 | 69 | empty |
| 2 | 375 | 0.63 | 0.78 | 41 | AHL |
| 3 | 306 | 0.59 | 0.78 | 40 | AHL |
| 4 | 178 | 0.54 | 0.79 | 31 | empty |
| 5 | 183 | 0.54 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1843 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2IMB · Clostridium botulinum Neurotoxin Serotype A Light Chain Inhibited by L-arginine… · 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 Q7B8V4
- Elsewhere: RCSB PDB 2IMB · PDBe 2IMB · UniProt Q7B8V4
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