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Crystal structure of KNI-10006 bound histo-aspartic protease (HAP) from Plasmodium falciparum
Analyse Crystal structure of KNI-10006 bound histo-aspartic protease (HAP) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FNU
- Type
- protein
- Length
- 1,304 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Plasmodium falciparum
- Molecule
- HAP protein
- UniProt
- Q8IM15
- Ligands
- 006
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · resolution 3 · 1 distinct chain · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | HAP protein | protein | 326 | 12% helix, 47% strand | Q8IM15 |
Ligands and binding sites
- 006 · (4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.78 | 0.80 | 105 | empty |
| 2 | 1001 | 0.78 | 0.79 | 103 | 006 |
| 3 | 609 | 0.71 | 0.78 | 67 | 006 |
| 4 | 195 | 0.58 | 0.80 | 23 | 006 |
| 5 | 168 | 0.50 | 0.78 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1464 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1427 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 323 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 296 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 68 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3FNU · Crystal structure of kni-10006 bound histo-aspartic protease (hap) from plasmodium… · the same entry in another collection · 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 Q8IM15
- Elsewhere: RCSB PDB 3FNU · PDBe 3FNU · UniProt Q8IM15
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