MolNFT v1 · #103923 · protein
Crystal structure of aminopeptidase N in complex with the phosphonic acid analogue of leucine (D-(S)-leup)
4PVB: “Crystal structure of aminopeptidase N in complex with the phosphonic acid analogue of leucine (D-(S)-leup)”. X-ray diffraction, 4 ligands (2WW, ZN, SO4), 9 pockets (best druggability 0.79). MolNFT v1 #103923 on GenesisL1: 3D…
- PDB
- 4PVB
- Type
- protein
- Length
- 864 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- Q9JYV4
- Ligands
- 2WW, ZN, SO4, PO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 864 | 45% helix, 23% strand | Q9JYV4 |
Ligands and binding sites
- 2WW · [(1S)-1-amino-3-methylbutyl]phosphonic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- PO4 · Phosphate ion · ion · 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 | 527 | 0.79 | 0.86 | 62 | empty |
| 2 | 453 | 0.76 | 0.85 | 63 | 2WW |
| 3 | 356 | 0.69 | 0.82 | 45 | PO4 |
| 4 | 470 | 0.65 | 0.77 | 48 | empty |
| 5 | 174 | 0.50 | 0.77 | 28 | empty |
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4PVB · Crystal structure of Aminopeptidase N in complex with the phosphonic acid analogue of… · the same entry in another collection · 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 Q9JYV4
- Elsewhere: RCSB PDB 4PVB · PDBe 4PVB · UniProt Q9JYV4
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