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Structure of plasmepsin II from plasmodium falciparum complexed with inhibitor PG394
Analyse Structure of plasmepsin II from plasmodium falciparum complexed with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YA8
- Type
- protein
- Length
- 1,315 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin-2
- EC
- 3.4.23.39
- UniProt
- P46925
- Ligands
- 49W
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Plasmepsin-2 (EC 3.4.23.39) | protein | 329 | 13% helix, 48% strand | P46925 |
| D | Plasmepsin-2 (EC 3.4.23.39) | protein | 328 | 14% helix, 46% strand | P46925 |
Ligands and binding sites
- 49W · N'-[(2S,3S)-3-hydroxy-1-phenyl-4-{[2-(pyridin-2-yl)propan-2-yl]amino}butan-2-yl]-N,N-dipropyl-5-(pyridin-1(2H)-yl)benzene-1,3-dicarboxamide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.76 | 0.78 | 97 | 49W |
| 2 | 387 | 0.62 | 0.77 | 45 | 49W |
| 3 | 413 | 0.62 | 0.76 | 50 | 49W, GOL |
| 4 | 299 | 0.56 | 0.76 | 29 | empty |
| 5 | 294 | 0.52 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 764 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 277 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 79 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4YA8 · structure of plasmepsin II from Plasmodium Falciparum complexed with inhibitor PG394 · the same entry in another collection · chain A against A, TM-score 1.00
- P46925 · AlphaFold monomer V2.0 prediction for plasmepsin-2 (P46925) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 P46925
- Elsewhere: RCSB PDB 4YA8 · PDBe 4YA8 · UniProt P46925
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