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Crystal structure of plasmepsin II, an aspartyl protease from plasmodium falciparum, in complex with a statine-based inhibitor
Analyse Crystal structure of plasmepsin II, an aspartyl protease from plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ME6
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin II
- EC
- 3.4.23.39
- UniProt
- P46925
- Ligands
- IVS
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmepsin II (EC 3.4.23.39) | protein | 329 | 11% helix, 43% strand | P46925 |
Ligands and binding sites
- IVS · 3-hydroxy-6-methyl-4-(3-methyl-2-(3-methyl-2-(3-methyl-butyrylamino)-butyrylamino)-butyrylamino)-heptanoic acid ethyl ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.66 | 0.79 | 43 | IVS |
| 2 | 373 | 0.62 | 0.77 | 43 | IVS |
| 3 | 174 | 0.51 | 0.78 | 25 | empty |
| 4 | 85 | 0.34 | 0.75 | 20 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1ME6 · Crystal structure of plasmepsin II, an aspartyl protease from plasmodium falciparum, in… · 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 A against A, TM-score 0.90
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 1ME6 · PDBe 1ME6 · UniProt P46925
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