Research workbench
1-cys peroxidoxin from plasmodium yoelli
Analyse 1-cys peroxidoxin from plasmodium yoelli in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XCC
- Type
- protein
- Length
- 871 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-cys peroxiredoxin
- UniProt
- Q86SB3
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-cys peroxiredoxin | protein | 219 | 30% helix, 26% strand | Q86SB3 |
| B, C | 1-cys peroxiredoxin | protein | 218 | 28% helix, 26% strand | Q86SB3 |
| D | 1-cys peroxiredoxin | protein | 216 | 28% helix, 26% strand | Q86SB3 |
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.80 | 0.82 | 123 | empty |
| 2 | 155 | 0.69 | 0.88 | 23 | empty |
| 3 | 200 | 0.58 | 0.80 | 27 | empty |
| 4 | 224 | 0.57 | 0.79 | 41 | empty |
| 5 | 145 | 0.56 | 0.82 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–D · 2645 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2633 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 121 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1XCC · 1-Cys peroxidoxin from Plasmodium Yoelli · 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 Q86SB3
- Elsewhere: RCSB PDB 1XCC · PDBe 1XCC · UniProt Q86SB3
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