Research workbench
Crystal structure of plasmodium falciparum aminopeptidase N in complex with (S)-N-hydroxy-4-methyl-2-(3-(3-METHYLBENZYL)UREIDO)PENTANAMIDE
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
- 5Y3I
- Type
- protein
- Length
- 890 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
- 8N3, MG, ZN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1 family aminopeptidase (EC 3.4.11.-) | protein | 890 | 45% helix, 22% strand | O96935 |
Ligands and binding sites
- 8N3 · (2R)-4-methyl-2-[(3-methylphenyl)methylcarbamoylamino]-N-oxidanyl-pentanamide · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.82 | 0.85 | 85 | GOL |
| 2 | 635 | 0.80 | 0.85 | 72 | MG, 8N3, GOL |
| 3 | 668 | 0.68 | 0.76 | 70 | MG |
| 4 | 354 | 0.60 | 0.77 | 48 | empty |
| 5 | 175 | 0.41 | 0.73 | 23 | empty |
Compared structures
- 5Y3I · 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 5Y3I · PDBe 5Y3I · UniProt O96935
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.