MolNFT v1 · #103577 · protein
Anthrax toxin lethal factor with bound small molecule inhibitor GM6001
4PKW: “Anthrax toxin lethal factor with bound small molecule inhibitor GM6001”. X-ray diffraction, 2 ligands (GM6, ZN), 3 pockets (best druggability 0.78). MolNFT v1 #103577 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PKW
- Type
- protein
- Length
- 491 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lethal factor
- EC
- 3.4.24.83
- UniProt
- P15917
- Ligands
- GM6, ZN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lethal factor (EC 3.4.24.83) | protein | 491 | 52% helix, 15% strand | P15917 |
Ligands and binding sites
- GM6 · 3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-trp-methylamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.78 | 0.80 | 90 | ZN, GM6, GOL |
| 2 | 159 | 0.55 | 0.80 | 18 | empty |
| 3 | 318 | 0.55 | 0.75 | 30 | empty |
Compared structures
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 4PKW · PDBe 4PKW · UniProt P15917
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