Research workbench
Human peroxiredoxin 2 oxidized (ss)
Analyse Human peroxiredoxin 2 oxidized (ss) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IJT
- Type
- protein
- Length
- 1,683 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin-2
- EC
- 1.11.1.15
- UniProt
- P32119
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 10 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 162 | 30% helix, 29% strand | P32119 |
| B | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 171 | 28% helix, 27% strand | P32119 |
| C | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 157 | 27% helix, 29% strand | P32119 |
| D | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 158 | 27% helix, 30% strand | P32119 |
| E | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 178 | 30% helix, 26% strand | P32119 |
| F | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 177 | 28% helix, 27% strand | P32119 |
| G | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 164 | 29% helix, 29% strand | P32119 |
| H | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 167 | 29% helix, 28% strand | P32119 |
| I | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 173 | 27% helix, 27% strand | P32119 |
| J | Peroxiredoxin-2 (EC 1.11.1.15) | protein | 176 | 28% helix, 27% strand | P32119 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.75 | 0.92 | 28 | empty |
| 2 | 221 | 0.73 | 0.88 | 47 | empty |
| 3 | 57 | 0.72 | 0.99 | 21 | empty |
| 4 | 447 | 0.72 | 0.82 | 60 | empty |
| 5 | 254 | 0.70 | 0.85 | 45 | empty |
Interfaces
14 interfaces between chains.
- E–F · 1938 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 1752 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1362 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 980 Ų buried · 13 hydrogen bonds · protein-protein
- F–H · 785 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 P32119
- Elsewhere: RCSB PDB 5IJT · PDBe 5IJT · UniProt P32119
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