MolNFT v1 · #112621 · protein
Crystal structure of pfa-M1 with virtual ligand inhibitor
4ZQT · M1 family aminopeptidase: “Crystal structure of pfa-M1 with virtual ligand inhibitor”. X-ray diffraction, 3 ligands (4QP, ZN, MG), 13 pockets (best druggability 0.80). MolNFT v1 #112621 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4ZQT
- 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
- 4QP, ZN, MG
- Pockets
- 13 · best druggability 0.80
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
- 4QP · (2R)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.80 | 0.87 | 76 | 4QP, ZN, GOL |
| 2 | 238 | 0.69 | 0.85 | 31 | empty |
| 3 | 82 | 0.64 | 0.90 | 22 | empty |
| 4 | 412 | 0.62 | 0.77 | 55 | empty |
| 5 | 122 | 0.61 | 0.86 | 20 | empty |
Compared structures
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 4ZQT · PDBe 4ZQT · UniProt O96935
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