Research workbench
Crystal structure of clostridium botulinum neurotoxin B complexed with an inhibitor (experiment 2)
Analyse Crystal structure of clostridium botulinum neurotoxin B complexed with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G9D
- Type
- protein
- Length
- 1,287 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B
- EC
- 3.4.24.69
- UniProt
- P10844
- Ligands
- BAB, ZN
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 1287 | 31% helix, 24% strand | P10844 |
Ligands and binding sites
- BAB · Bis(5-amidino-benzimidazolyl)methane · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.80 | 0.83 | 68 | ZN, BAB |
| 2 | 476 | 0.77 | 0.85 | 68 | empty |
| 3 | 882 | 0.75 | 0.79 | 81 | BAB |
| 4 | 340 | 0.67 | 0.81 | 38 | empty |
| 5 | 74 | 0.60 | 0.90 | 21 | empty |
Compared structures
- 1G9D · Crystal structure of clostridium botulinum neurotoxin B complexed with an inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P10844 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type B (P10844) · a predicted model of the same protein · chain A against A, TM-score 0.67
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 P10844
- Elsewhere: RCSB PDB 1G9D · PDBe 1G9D · UniProt P10844
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