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X-ray crystal structure of the aspartic protease plasmepsin 4 from the malarial parasite plasmodium malariae bound to an allophenylnorstatine based inhibitor
Analyse X-ray crystal structure of the aspartic protease plasmepsin 4 from the malarial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ANL
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin IV
- UniProt
- O60990
- Ligands
- JE2
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmepsin IV | protein | 327 | 11% helix, 44% strand | O60990 |
Ligands and binding sites
- JE2 · (4R)-3-{(2S,3S)-2-hydroxy-3-[(3-hydroxy-2-methylbenzoyl)amino]-4-phenylbutanoyl}-5,5-dimethyl-N-(2-methylbenzyl)-1,3-thiazolidine-4-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.68 | 0.77 | 56 | JE2 |
| 2 | 554 | 0.65 | 0.76 | 57 | JE2 |
| 3 | 132 | 0.51 | 0.80 | 29 | empty |
| 4 | 126 | 0.50 | 0.80 | 22 | empty |
| 5 | 163 | 0.49 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2ANL · X-ray crystal structure of the aspartic protease plasmepsin 4 from the malarial parasite… · the same entry in another collection · chain A against A, TM-score 1.00
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 O60990
- Elsewhere: RCSB PDB 2ANL · PDBe 2ANL · UniProt O60990
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