Research workbench
Crystal structure of the anthrax lethal factor complexed with small molecule inhibitor nsc 12155
Analyse Crystal structure of the anthrax lethal factor complexed with small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PWP
- Type
- protein
- Length
- 1,475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lethal factor
- EC
- 3.4.24.83
- UniProt
- P15917
- Ligands
- NSC, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lethal factor (EC 3.4.24.83) | protein | 732 | 51% helix, 13% strand | P15917 |
| B | Lethal factor (EC 3.4.24.83) | protein | 743 | 54% helix, 12% strand | P15917 |
Ligands and binding sites
- NSC · N,N'-bis(4-amino-2-methylquinolin-6-yl)urea · 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
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.86 | 0.90 | 76 | empty |
| 2 | 881 | 0.71 | 0.76 | 95 | NSC |
| 3 | 252 | 0.64 | 0.82 | 28 | empty |
| 4 | 208 | 0.62 | 0.82 | 31 | empty |
| 5 | 174 | 0.62 | 0.84 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1380 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1PWP · Crystal Structure of the Anthrax Lethal Factor complexed with Small Molecule Inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P15917 · AlphaFold monomer V2.0 prediction for lethal factor (P15917) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P15917
- Elsewhere: RCSB PDB 1PWP · PDBe 1PWP · UniProt P15917
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