MolNFT v1 · #140161 · protein
Crystal structure of plasmodium falciparum aminopeptidase N in complex with actinonin
5Y1X · M1 family aminopeptidase: “Crystal structure of plasmodium falciparum aminopeptidase N in complex with actinonin”. X-ray diffraction, 3 ligands (BB2, ZN, MG), 9 pockets (best druggability 0.84). MolNFT v1 #140161 on GenesisL1: 3D…
- PDB
- 5Y1X
- Type
- protein
- Length
- 891 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
- BB2, ZN, MG
- Pockets
- 9 · best druggability 0.84
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 | 891 | 45% helix, 22% strand | O96935 |
Ligands and binding sites
- BB2 · Actinonin · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.84 | 0.85 | 89 | GOL |
| 2 | 749 | 0.81 | 0.85 | 83 | ZN, BB2 |
| 3 | 625 | 0.68 | 0.77 | 61 | empty |
| 4 | 52 | 0.45 | 0.84 | 21 | empty |
| 5 | 159 | 0.42 | 0.74 | 24 | empty |
Compared structures
- 5Y1X · Crystal structure of Plasmodium falciparum aminopeptidase N in complex with actinonin · 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 5Y1X · PDBe 5Y1X · UniProt O96935
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