Research workbench
The crystal structure of plasmodium vivax 2-cys peroxiredoxin
Analyse The crystal structure of plasmodium vivax 2-cys peroxiredoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H66
- Type
- protein
- Length
- 1,684 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pv-PF14_0368
- UniProt
- A5K421
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 8 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Pv-PF14_0368 | protein | 167 | 31% helix, 28% strand | A5K421 |
| B, G | Pv-PF14_0368 | protein | 171 | 29% helix, 27% strand | A5K421 |
| C | Pv-PF14_0368 | protein | 170 | 29% helix, 27% strand | A5K421 |
| D | Pv-PF14_0368 | protein | 169 | 30% helix, 28% strand | A5K421 |
| E | Pv-PF14_0368 | protein | 161 | 28% helix, 29% strand | A5K421 |
| F | Pv-PF14_0368 | protein | 168 | 30% helix, 28% strand | A5K421 |
| I | Pv-PF14_0368 | protein | 177 | 29% helix, 27% strand | A5K421 |
| J | Pv-PF14_0368 | protein | 163 | 29% helix, 29% strand | A5K421 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.68 | 0.80 | 54 | empty |
| 2 | 334 | 0.65 | 0.80 | 46 | empty |
| 3 | 185 | 0.65 | 0.85 | 30 | empty |
| 4 | 197 | 0.64 | 0.84 | 35 | empty |
| 5 | 324 | 0.64 | 0.79 | 51 | empty |
Interfaces
10 interfaces between chains.
- I–J · 1513 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1415 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1403 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1370 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1251 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2H66 · The Crystal Structure of Plasmodium Vivax 2-Cys peroxiredoxin · 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 A5K421
- Elsewhere: RCSB PDB 2H66 · PDBe 2H66 · UniProt A5K421
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