MolNFT v1 · #13919 · protein
Crystal structure of plasmepsin IV from P. falciparum in complex with pepstatin a
1LS5: “Crystal structure of plasmepsin IV from P. falciparum in complex with pepstatin a”. X-ray diffraction, 1 ligand (IVA), 3 pockets (best druggability 0.87). MolNFT v1 #13919 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1LS5
- Type
- protein
- Length
- 666 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin IV; Pepstatin
- UniProt
- Q8IM16
- Ligands
- IVA
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmepsin IV | protein | 328 | 11% helix, 38% strand | Q8IM16 |
| C, D | Pepstatin | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- IVA · Isovaleric acid · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.87 | 0.88 | 100 | IVA |
| 2 | 56 | 0.54 | 0.88 | 13 | empty |
| 3 | 58 | 0.30 | 0.76 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1193 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 620 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 566 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 104 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified, 2 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 1LS5 · Crystal structure of plasmepsin IV from P. falciparum in complex with pepstatin A · 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 Q8IM16
- Elsewhere: RCSB PDB 1LS5 · PDBe 1LS5 · UniProt Q8IM16
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