MolNFT v1 · #103951 · protein
Crystal structure of aminopeptidase N in complex with phosphonic acid analogue of homophenylalanine L-(R)-hphep
4PW4: “Crystal structure of aminopeptidase N in complex with phosphonic acid analogue of homophenylalanine…”. X-ray diffraction, 3 ligands (2X0, ZN, SO4), 9 pockets (best druggability 0.83). MolNFT v1 #103951 on GenesisL1: 3D structure…
- PDB
- 4PW4
- Type
- protein
- Length
- 865 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
- 2X0, ZN, SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 865 | 45% helix, 22% strand | Q9JYV4 |
Ligands and binding sites
- 2X0 · [(1R)-1-amino-3-phenylpropyl]phosphonic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A
- IMD · Imidazole · additive · chains A
- GOL · Glycerol · additive · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.83 | 0.86 | 100 | 2X0, SO4 |
| 2 | 225 | 0.66 | 0.84 | 28 | SO4 |
| 3 | 299 | 0.58 | 0.77 | 30 | empty |
| 4 | 76 | 0.53 | 0.86 | 20 | empty |
| 5 | 65 | 0.52 | 0.86 | 20 | empty |
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4PW4 · Crystal structure of Aminopeptidase N in complex with 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 4PW4 · PDBe 4PW4 · UniProt Q9JYV4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.