MolNFT v1 · #112827 · protein
X-ray crystal structure of pfa-M1 in complex with hydroxamic acid- based inhibitor 10S
4ZX6 · M1 family aminopeptidase: “X-ray crystal structure of pfa-M1 in complex with hydroxamic acid- based inhibitor 10S”. X-ray diffraction, 3 ligands (4U6, ZN, MG), 13 pockets (best druggability 0.80). MolNFT v1 #112827 on GenesisL1: 3D…
- PDB
- 4ZX6
- Type
- protein
- Length
- 888 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
- 4U6, ZN, MG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1 family aminopeptidase (EC 3.4.11.-) | protein | 888 | 45% helix, 22% strand | O96935 |
Ligands and binding sites
- 4U6 · N-{(1R)-2-(hydroxyamino)-1-[3'-(N'-hydroxycarbamimidoyl)biphenyl-4-yl]-2-oxoethyl}-2,2-dimethylpropanamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.80 | 0.87 | 66 | ZN, 4U6, DMS |
| 2 | 292 | 0.74 | 0.87 | 46 | empty |
| 3 | 82 | 0.66 | 0.92 | 23 | empty |
| 4 | 133 | 0.62 | 0.86 | 27 | empty |
| 5 | 285 | 0.56 | 0.77 | 43 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4ZX6 · X-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 10s · 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 4ZX6 · PDBe 4ZX6 · UniProt O96935
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.