MolNFT v1 · #116047 · protein

Anthrax toxin lethal factor with hydroxamic acid inhibitor

5D1T: “Anthrax toxin lethal factor with hydroxamic acid inhibitor”. X-ray diffraction, 2 ligands (56R, ZN), 4 pockets (best druggability 0.71). MolNFT v1 #116047 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5D1T
Type: protein
Length: 488 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: 56R, ZN
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lethal factor (EC 3.4.24.83)	protein	488	51% helix, 15% strand	P15917

Ligands and binding sites

56R · N~2~-[3-(aminomethyl)benzyl]-N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide · ligand · chains A
ZN · Zinc ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	504	0.71	0.81	45	empty
2	459	0.66	0.78	49	56R
3	157	0.59	0.83	20	empty
4	266	0.53	0.76	28	empty

Compared structures

5D1T · Anthrax toxin lethal factor with hydroxamic acid 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 A against A, TM-score 0.98

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 5D1T · PDBe 5D1T · UniProt P15917

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