Research workbench
Peroxiredoxin (C207S) from aeropyrum pernix K1 complexed with hydrogen peroxide
Analyse Peroxiredoxin (C207S) from aeropyrum pernix K1 complexed with hydrogen peroxide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A2V
- Type
- protein
- Length
- 2,424 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable peroxiredoxin
- EC
- 1.11.1.15
- UniProt
- Q9Y9L0
- Ligands
- PER
- Pockets
- 20 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G, J | Probable peroxiredoxin (EC 1.11.1.15) | protein | 243 | 36% helix, 24% strand | Q9Y9L0 |
| B, E, H, I | Probable peroxiredoxin (EC 1.11.1.15) | protein | 242 | 34% helix, 24% strand | Q9Y9L0 |
| D | Probable peroxiredoxin (EC 1.11.1.15) | protein | 240 | 35% helix, 24% strand | Q9Y9L0 |
| F | Probable peroxiredoxin (EC 1.11.1.15) | protein | 244 | 34% helix, 24% strand | Q9Y9L0 |
Ligands and binding sites
- PER · Peroxide ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.60 | 0.79 | 46 | PER |
| 2 | 317 | 0.59 | 0.77 | 53 | PER |
| 3 | 293 | 0.58 | 0.77 | 40 | PER |
| 4 | 323 | 0.57 | 0.76 | 44 | PER |
| 5 | 278 | 0.57 | 0.77 | 53 | PER |
Interfaces
20 interfaces between chains.
- G–H · 3572 Ų buried · 57 hydrogen bonds · protein-protein
- I–J · 3566 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 3557 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 3537 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3506 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 3A2V · Peroxiredoxin (C207S) from Aeropyrum pernix K1 complexed with hydrogen peroxide · the same entry in another collection · chain J against J, TM-score 1.00
- Q9Y9L0 · AlphaFold monomer V2.0 prediction for peroxiredoxin (Q9Y9L0) · a predicted model of the same protein · chain B 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 Q9Y9L0
- Elsewhere: RCSB PDB 3A2V · PDBe 3A2V · UniProt Q9Y9L0
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