MolNFT v1 · #18681 · protein
Crystal structure of anthrax lethal factor complexed with thioacetyl-tyr-pro-met-amide, a metal-chelating peptidyl small molecule inhibitor
1PWQ: “Crystal structure of anthrax lethal factor complexed with thioacetyl-tyr-pro-met-amide, a metal-chelating…”. X-ray diffraction, 2 ligands (SD2, ZN), 18 pockets (best druggability 0.87). MolNFT v1 #18681 on GenesisL1: 3D structure…
- PDB
- 1PWQ
- Type
- protein
- Length
- 1,466 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
- SD2, ZN
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lethal factor (EC 3.4.24.83) | protein | 732 | 49% helix, 11% strand | P15917 |
| B | Lethal factor (EC 3.4.24.83) | protein | 734 | 50% helix, 12% strand | P15917 |
Ligands and binding sites
- SD2 · N-(sulfanylacetyl)tyrosylprolylmethioninamide · 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
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.87 | 0.89 | 135 | empty |
| 2 | 861 | 0.72 | 0.77 | 94 | SD2 |
| 3 | 526 | 0.64 | 0.76 | 55 | empty |
| 4 | 289 | 0.63 | 0.80 | 34 | empty |
| 5 | 169 | 0.63 | 0.85 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1416 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1PWQ · Crystal structure of Anthrax Lethal Factor complexed with Thioacetyl-Tyr-Pro-Met-Amide, a… · 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 1PWQ · PDBe 1PWQ · UniProt P15917
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