MolNFT v1 · #18683 · protein

Crystal structure of anthrax lethal factor complexed with (3-(N- hydroxycarboxamido)-2-isobutylpropanoyl-TRP-methylamide), a known small molecule inhibitor of matrix metalloproteases.

1PWU: “Crystal structure of anthrax lethal factor complexed with (3-(N…”. X-ray diffraction, 2 ligands (GM6, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #18683 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PWU
Type: protein
Length: 1,483 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lethal factor
EC: 3.4.24.-
UniProt: P15917
Ligands: GM6, ZN
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lethal factor (EC 3.4.24.-)	protein	747	52% helix, 13% strand	P15917
B	Lethal factor (EC 3.4.24.-)	protein	736	54% helix, 13% strand	P15917

Ligands and binding sites

GM6 · 3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-trp-methylamide · 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	751	0.84	0.88	82	empty
2	416	0.79	0.88	45	empty
3	609	0.72	0.79	72	GM6
4	57	0.69	0.97	18	empty
5	57	0.68	0.96	18	empty

Interfaces

1 interface between chains.

A–B · 1319 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1PWU · Crystal Structure of Anthrax Lethal Factor complexed with… · 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 1PWU · PDBe 1PWU · UniProt P15917

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