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Crystal structure of plasmepsin from P. falciparum in complex with inhibitor RS367
Analyse Crystal structure of plasmepsin 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
- 1LEE
- 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
- R36
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmepsin 2 (EC 3.4.23.39) | protein | 331 | 13% helix, 47% strand | P46925 |
Ligands and binding sites
- R36 · 4-amino-N-{4-[2-(2,6-dimethyl-phenoxy)-acetylamino]-3-hydroxy-1-isobutyl-5-phenyl-pentyl}-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 | 321 | 0.60 | 0.77 | 39 | R36 |
| 2 | 131 | 0.45 | 0.77 | 25 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1LEE · Crystal structure of plasmepsin from P. falciparum in complex with inhibitor RS367 · 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 0.91
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 1LEE · PDBe 1LEE · UniProt P46925
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