MolNFT v1 · #112429 · protein
Plasmepsin V from plasmodium vivax bound to a transition state mimetic (wehi-842)
4ZL4 · Aspartic protease PM5: “Plasmepsin V from plasmodium vivax bound to a transition state mimetic (wehi-842)”. X-ray diffraction, 3 ligands (4PK, 4PF, SO4), 5 pockets (best druggability 0.74). MolNFT v1 #112429 on GenesisL1: 3D…
- PDB
- 4ZL4
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartic protease PM5
- UniProt
- Q6PRR9
- Ligands
- 4PK, 4PF, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartic protease PM5 | protein | 395 | 19% helix, 38% strand | Q6PRR9 |
Ligands and binding sites
- 4PK · N-[(benzyloxy)carbonyl]-O-carbamimidamido-L-homoseryl-N-{(3S,4S)-3-hydroxy-6-methyl-1-oxo-1-[(2-phenylethyl)amino]heptan-4-yl}-L-valinamide · ligand · 2 copies · chains A, B
- 4PF · (2R)-1-[(2R)-2-(2-methoxyethoxy)propoxy]propan-2-amine · ligand · chains B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.74 | 0.77 | 88 | empty |
| 2 | 498 | 0.68 | 0.79 | 62 | 4PK, EDO |
| 3 | 480 | 0.67 | 0.78 | 64 | 4PK, SO4, EDO |
| 4 | 84 | 0.41 | 0.78 | 14 | empty |
| 5 | 66 | 0.36 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 544 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4ZL4 · Plasmepsin V from Plasmodium vivax bound to a transition state mimetic (WEHI-842) · 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 Q6PRR9
- Elsewhere: RCSB PDB 4ZL4 · PDBe 4ZL4 · UniProt Q6PRR9
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