MolNFT v1 · #40278 · protein
Clostridium botulinum neurotoxin serotype a light chain inhibited by 2,4-dichlorocinnamic hydroxamate
2IMA · Botulinum neurotoxin a light-chain: “Clostridium botulinum neurotoxin serotype a light chain inhibited by 2,4-dichlorocinnamic hydroxamate”. X-ray diffraction, 2 ligands (GB4, ZN), 9 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 2IMA
- Type
- protein
- Length
- 805 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
- GB4, ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin a light-chain (EC 3.4.24.69) | protein | 402 | 31% helix, 19% strand | Q7B8V4 |
| B | Botulinum neurotoxin a light-chain (EC 3.4.24.69) | protein | 403 | 32% helix, 18% strand | Q7B8V4 |
Ligands and binding sites
- GB4 · (2E)-3-(2,4-dichlorophenyl)-N-hydroxyacrylamide · 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
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 | 904 | 0.76 | 0.79 | 67 | empty |
| 2 | 415 | 0.66 | 0.79 | 44 | GB4 |
| 3 | 243 | 0.61 | 0.81 | 31 | GB4 |
| 4 | 250 | 0.56 | 0.78 | 35 | empty |
| 5 | 186 | 0.52 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1678 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2IMA · Clostridium botulinum Neurotoxin Serotype A Light Chain Inhibited by 2,4-dichlorocinnamic… · 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 2IMA · PDBe 2IMA · UniProt Q7B8V4
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