Research workbench
Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2,6-diethylphenyl)ureido)- N-hydroxy-4-methylpentanamide
Analyse Crystal structure of Plasmodium falciparum aminopeptidase N in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y1V
- Type
- protein
- Length
- 890 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.62
- Source
- Plasmodium falciparum
- Molecule
- M1 family aminopeptidase
- EC
- 3.4.11.-
- UniProt
- O96935
- Ligands
- 8LO, MG, ZN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.62 · 1 distinct chain · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1 family aminopeptidase (EC 3.4.11.-) | protein | 890 | 46% helix, 22% strand | O96935 |
Ligands and binding sites
- 8LO · (2R)-2-[(2,6-diethylphenyl)carbamoylamino]-4-methyl-N-oxidanyl-pentanamide · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.83 | 0.84 | 131 | 8LO, GOL |
| 2 | 813 | 0.79 | 0.83 | 66 | empty |
| 3 | 67 | 0.42 | 0.81 | 18 | empty |
| 4 | 166 | 0.41 | 0.73 | 23 | empty |
| 5 | 116 | 0.41 | 0.76 | 18 | empty |
Compared structures
- 5Y1V · Crystal structure of plasmodium falciparum aminopeptidase N in complex with… · 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 5Y1V · PDBe 5Y1V · UniProt O96935
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