Research workbench
X-ray crystal structure of the anthrax lethal factor bound to a small molecule inhibitor, bi-MFM3, 3-{5-[5-(4-chloro- phenyl)-furan-2-ylmethylene]-4-oxo-2-thioxo-thiazolidin-3- yl}-propionic acid.
Analyse X-ray crystal structure of the anthrax lethal factor bound to a small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZXV
- Type
- protein
- Length
- 1,464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lethal factor
- EC
- 3.4.24.83
- Ligands
- MFM, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lethal factor (EC 3.4.24.83) | protein | 728 | 52% helix, 13% strand | — |
| B | Lethal factor (EC 3.4.24.83) | protein | 736 | 52% helix, 14% strand | — |
Ligands and binding sites
- MFM · (E)-3-(5((5-(4-chlorophenyl)furan-2-yl)methylene)-4-oxo-2-thioxothiazolidin-3-yl)propanoic acid · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.86 | 0.90 | 86 | empty |
| 2 | 937 | 0.72 | 0.76 | 90 | empty |
| 3 | 516 | 0.69 | 0.79 | 63 | MFM |
| 4 | 385 | 0.67 | 0.80 | 52 | empty |
| 5 | 173 | 0.60 | 0.83 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1377 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1ZXV · X-Ray Crystal Structure of the Anthrax Lethal Factor Bound to a Small Molecule Inhibitor… · 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
- Elsewhere: RCSB PDB 1ZXV · PDBe 1ZXV
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