Research workbench
Crystal structure of plasmepsin II from P falciparum in complex with inhibitor EH58
Analyse Crystal structure of plasmepsin II from P falciparum in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LF3
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin 2
- EC
- 3.4.23.39
- UniProt
- P46925
- Ligands
- EH5
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmepsin 2 (EC 3.4.23.39) | protein | 331 | 13% helix, 46% strand | P46925 |
Ligands and binding sites
- EH5 · N-(1-benzyl-3-{[3-(1,3-dioxo-1,3-dihydro-isoindol-2-yl)-propionyl]-[2-(hexahydro-benzo[1,3]dioxol-5-yl)-ethyl]-amino}-2-hydroxy-propyl)-4-benzyloxy-3,5-dimethoxy-benzamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.59 | 0.77 | 34 | EH5 |
| 2 | 151 | 0.46 | 0.77 | 21 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1LF3 · Crystal structure of plasmepsin II from P falciparum in complex with inhibitor EH58 · 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 0.93
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 1LF3 · PDBe 1LF3 · UniProt P46925
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