Research workbench
Crystal structure of plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2-CHLOROBENZYL)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
- 5Y1K
- 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
- B1B, MG, ZN
- Pockets
- 10 · 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
- B1B · (2S)-2-[(2-chlorophenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 6 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.82 | 0.85 | 105 | ZN, MG, GOL, B1B |
| 2 | 624 | 0.80 | 0.85 | 59 | GOL |
| 3 | 208 | 0.64 | 0.83 | 28 | empty |
| 4 | 173 | 0.42 | 0.73 | 25 | empty |
| 5 | 57 | 0.42 | 0.82 | 16 | empty |
Compared structures
- 5Y1K · 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 5Y1K · PDBe 5Y1K · UniProt O96935
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