MolNFT v1 · #117108 · protein
The crystal structure of aminopeptidase N in complex with N-benzyl-1, 2-diaminoethylphosphonic acid
5DYF: “The crystal structure of aminopeptidase N in complex with N-benzyl-1, 2-diaminoethylphosphonic acid”. X-ray diffraction, 3 ligands (5HR, ZN, SO4), 10 pockets (best druggability 0.83). MolNFT v1 #117108 on GenesisL1: 3D structure…
- PDB
- 5DYF
- 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
- 5HR, ZN, SO4
- Pockets
- 10 · 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
- 5HR · [(1R)-1-amino-2-(benzylamino)ethyl]phosphonic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.83 | 0.86 | 80 | SO4, 5HR |
| 2 | 338 | 0.69 | 0.83 | 48 | SO4, GOL |
| 3 | 200 | 0.66 | 0.84 | 30 | SO4 |
| 4 | 454 | 0.64 | 0.77 | 44 | empty |
| 5 | 152 | 0.60 | 0.84 | 38 | empty |
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5DYF · The crystal structure of Aminopeptidase N in complex with… · 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 5DYF · PDBe 5DYF · UniProt Q9JYV4
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