Research workbench
Crystal structure of methylated PVS25, an ookinete protein from plasmodium vivax
Analyse Crystal structure of methylated PVS25, an ookinete protein from plasmodium vivax in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z1Y
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ookinete surface protein PVS25
- UniProt
- O96555
- Ligands
- YB
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ookinete surface protein PVS25 | protein | 177 | 3% helix, 49% strand | O96555 |
| B | Ookinete surface protein PVS25 | protein | 175 | 3% helix, 47% strand | O96555 |
Ligands and binding sites
- YB · Ytterbium (III) ion · metal · 9 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.65 | 0.81 | 37 | YB |
| 2 | 326 | 0.61 | 0.78 | 36 | empty |
| 3 | 295 | 0.59 | 0.78 | 33 | empty |
| 4 | 369 | 0.56 | 0.74 | 36 | empty |
| 5 | 171 | 0.51 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 625 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 22 disulfide (methylation, disulfide).
Compared structures
- 1Z1Y · Crystal structure of Methylated Pvs25, an ookinete protein from Plasmodium vivax · 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 O96555
- Elsewhere: RCSB PDB 1Z1Y · PDBe 1Z1Y · UniProt O96555
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.