MolNFT v1 · #18157 · protein
Proplasmepsin II from plasmodium falciparum
1PFZ: “Proplasmepsin II from plasmodium falciparum”. X-ray diffraction, 14 pockets (best druggability 0.74). MolNFT v1 #18157 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1PFZ
- Type
- protein
- Length
- 1,464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proplasmepsin II
- EC
- 3.4.23.39
- UniProt
- P46925
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proplasmepsin II (EC 3.4.23.39) | protein | 370 | 18% helix, 38% strand | P46925 |
| B | Proplasmepsin II (EC 3.4.23.39) | protein | 369 | 19% helix, 40% strand | P46925 |
| C | Proplasmepsin II (EC 3.4.23.39) | protein | 356 | 19% helix, 40% strand | P46925 |
| D | Proplasmepsin II (EC 3.4.23.39) | protein | 369 | 18% helix, 40% strand | P46925 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.74 | 0.77 | 120 | empty |
| 2 | 588 | 0.70 | 0.79 | 56 | empty |
| 3 | 453 | 0.64 | 0.77 | 49 | GOL |
| 4 | 244 | 0.62 | 0.80 | 41 | empty |
| 5 | 174 | 0.61 | 0.84 | 31 | empty |
Interfaces
5 interfaces between chains.
- B–D · 872 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 646 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 641 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 145 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 136 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 1PFZ · PDBe 1PFZ · UniProt P46925
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