Research workbench
Crystal structure of plasmodium falciparum aminopeptidase N in complex with (S)-N-hydroxy-4-methyl-2-(3-( O-TOLYL)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
- 5Y1R
- 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
- 8KR, MG, ZN
- Pockets
- 12 · best druggability 0.79
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
- 8KR · (2R)-4-methyl-2-[(2-methylphenyl)carbamoylamino]-N-oxidanyl-pentanamide · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.79 | 0.87 | 53 | ZN, 8KR |
| 2 | 357 | 0.75 | 0.86 | 40 | GOL |
| 3 | 81 | 0.69 | 0.94 | 21 | empty |
| 4 | 696 | 0.69 | 0.77 | 63 | empty |
| 5 | 113 | 0.61 | 0.86 | 24 | empty |
Compared structures
- 5Y1R · 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 5Y1R · PDBe 5Y1R · UniProt O96935
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