Research workbench
Plasmoredoxin, a redox-active protein unique for malaria parasites
Analyse Plasmoredoxin, a redox-active protein unique for malaria parasites in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AOO
- Type
- protein
- Length
- 648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmoredoxin
- UniProt
- Q8I224
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmoredoxin | protein | 168 | 40% helix, 21% strand | Q8I224 |
| B | Plasmoredoxin | protein | 165 | 42% helix, 21% strand | Q8I224 |
| C | Plasmoredoxin | protein | 155 | 39% helix, 23% strand | Q8I224 |
| D | Plasmoredoxin | protein | 160 | 41% helix, 23% strand | Q8I224 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 16 copies · chains A, B, C, D
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, C, B, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, D
- GOL · Glycerol · additive · chains A
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 | 1199 | 0.82 | 0.83 | 116 | PEG |
| 2 | 174 | 0.75 | 0.92 | 31 | P6G, PGE |
| 3 | 173 | 0.75 | 0.92 | 29 | PEG, P6G |
| 4 | 54 | 0.68 | 0.96 | 19 | empty |
| 5 | 103 | 0.37 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- B–D · 851 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 848 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 842 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 836 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 249 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7AOO · Plasmoredoxin, a redox-active protein unique for malaria parasites · the same entry in another collection · chain D against D, 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 Q8I224
- Elsewhere: RCSB PDB 7AOO · PDBe 7AOO · UniProt Q8I224
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