MolNFT v1 · #112825 · protein
X-ray crystal structure of pfa-M1 in complex with hydroxamic acid- based inhibitor 10O
4ZX4 · M1 family aminopeptidase: “X-ray crystal structure of pfa-M1 in complex with hydroxamic acid- based inhibitor 10O”. X-ray diffraction, 4 ligands (4TL, ZN, MG), 9 pockets (best druggability 0.85). MolNFT v1 #112825 on GenesisL1: 3D…
- PDB
- 4ZX4
- Type
- protein
- Length
- 889 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M1 family aminopeptidase
- EC
- 3.4.11.-
- UniProt
- O96935
- Ligands
- 4TL, ZN, MG, PO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1 family aminopeptidase (EC 3.4.11.-) | protein | 889 | 45% helix, 21% strand | O96935 |
Ligands and binding sites
- 4TL · N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluorobiphenyl-4-yl)ethyl]-2,2-dimethylpropanamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.85 | 0.86 | 112 | 4TL, ZN, GOL, DMS |
| 2 | 77 | 0.68 | 0.93 | 21 | empty |
| 3 | 416 | 0.63 | 0.77 | 58 | GOL |
| 4 | 123 | 0.57 | 0.84 | 21 | empty |
| 5 | 253 | 0.49 | 0.74 | 27 | empty |
Compared structures
- 4ZX4 · X-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 10o · the same entry in another collection · chain A against A, TM-score 1.00
- O96935 · AlphaFold monomer V2.0 prediction for M1 family aminopeptidase (O96935) · a predicted model of the same protein · 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
- Every structure of UniProt O96935
- Elsewhere: RCSB PDB 4ZX4 · PDBe 4ZX4 · UniProt O96935
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