Research workbench
Crystal structure of human peroxiredoxin I in complex with sulfiredoxin
Analyse Crystal structure of human peroxiredoxin I in complex with sulfiredoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RII
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin-1; Sulfiredoxin-1
- EC
- 1.11.1.15, 1.8.98.2
- UniProt
- Q06830, Q9BYN0
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxiredoxin-1 (EC 1.11.1.15) | protein | 184 | 27% helix, 25% strand | Q06830 |
| B | Peroxiredoxin-1 (EC 1.11.1.15) | protein | 185 | 27% helix, 25% strand | Q06830 |
| X | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 106 | 36% helix, 26% strand | Q9BYN0 |
| Y | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 99 | 35% helix, 28% strand | Q9BYN0 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains X, B, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.74 | 0.83 | 61 | PO4 |
| 2 | 536 | 0.73 | 0.81 | 66 | PO4 |
| 3 | 54 | 0.71 | 0.98 | 22 | empty |
| 4 | 118 | 0.46 | 0.79 | 26 | empty |
| 5 | 88 | 0.39 | 0.77 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–Y · 988 Ų buried · 9 hydrogen bonds · protein-protein
- B–X · 977 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 936 Ų buried · 17 hydrogen bonds · protein-protein
- B–Y · 770 Ų buried · 6 hydrogen bonds · protein-protein
- A–X · 713 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2RII · Crystal Structure of Human Peroxiredoxin I in complex with Sulfiredoxin · the same entry in another collection · chain Y against Y, TM-score 1.00
- Q9BYN0 · AlphaFold monomer V2.0 prediction for sulfiredoxin-1 (Q9BYN0) · a predicted model of the same protein · chain Y against A, TM-score 0.95
- Q06830 · AlphaFold monomer V2.0 prediction for peroxiredoxin-1 (Q06830) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q06830
- Every structure of UniProt Q9BYN0
- Elsewhere: RCSB PDB 2RII · PDBe 2RII · UniProt Q06830 · UniProt Q9BYN0
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