MolNFT v1 · #19707 · protein
Crystal structure of the P. vivax aspartic proteinase plasmepsin complexed with the inhibitor pepstatin a
1QS8: “Crystal structure of the P. vivax aspartic proteinase plasmepsin complexed with the inhibitor pepstatin a”. X-ray diffraction, 1 ligand (IVA), 6 pockets (best druggability 0.65). MolNFT v1 #19707 on GenesisL1: 3D structure, binding…
- PDB
- 1QS8
- Type
- protein
- Length
- 665 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin; Pepstatin a
- Ligands
- IVA
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmepsin | protein | 327 | 13% helix, 47% strand | — |
| B | Plasmepsin | protein | 328 | 14% helix, 47% strand | — |
| C, D | Pepstatin a | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- IVA · Isovaleric acid · ligand · 2 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.65 | 0.81 | 45 | empty |
| 2 | 414 | 0.61 | 0.76 | 48 | empty |
| 3 | 300 | 0.57 | 0.77 | 48 | IVA |
| 4 | 219 | 0.52 | 0.76 | 24 | IVA |
| 5 | 101 | 0.41 | 0.77 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 628 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 601 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 61 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 49 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified, 2 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 1QS8 · Crystal structure of the P. vivax aspartic proteinase plasmepsin complexed with the… · 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
- Elsewhere: RCSB PDB 1QS8 · PDBe 1QS8
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