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Crystal structure of kni-10006 complex of plasmepsin I (pmi) from plasmodium falciparum
Analyse Crystal structure of kni-10006 complex of plasmepsin I (pmi) from plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QS1
- Type
- protein
- Length
- 1,306 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin-1
- EC
- 3.4.23.38
- UniProt
- P39898
- Ligands
- 006
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmepsin-1 (EC 3.4.23.38) | protein | 327 | 10% helix, 47% strand | P39898 |
| C, D | Plasmepsin-1 (EC 3.4.23.38) | protein | 326 | 11% helix, 45% strand | P39898 |
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
- GOL · Glycerol · additive · 10 copies · chains B, C, D, 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 | 593 | 0.78 | 0.84 | 58 | 006 |
| 2 | 550 | 0.78 | 0.84 | 58 | 006, GOL |
| 3 | 562 | 0.77 | 0.83 | 50 | 006 |
| 4 | 450 | 0.73 | 0.83 | 57 | empty |
| 5 | 372 | 0.72 | 0.83 | 43 | 006 |
Interfaces
6 interfaces between chains.
- C–D · 986 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 753 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 522 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 509 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 319 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3QS1 · Crystal structure of KNI-10006 complex of Plasmepsin I (PMI) from Plasmodium falciparum · the same entry in another collection · chain A against A, TM-score 1.00
- P39898 · AlphaFold monomer V2.0 prediction for plasmepsin-1 (P39898) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P39898
- Elsewhere: RCSB PDB 3QS1 · PDBe 3QS1 · UniProt P39898
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