Research workbench
Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from aeropyrum pernix K1 (sulfonic acid form)
Analyse Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NVL
- Type
- protein
- Length
- 2,416 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
- Pockets
- 20 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, G, H, I, J | Probable peroxiredoxin (EC 1.11.1.15) | protein | 242 | 38% helix, 24% strand | Q9Y9L0 |
| B | Probable peroxiredoxin (EC 1.11.1.15) | protein | 240 | 37% helix, 24% strand | Q9Y9L0 |
| C | Probable peroxiredoxin (EC 1.11.1.15) | protein | 240 | 37% helix, 24% strand | Q9Y9L0 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.56 | 0.76 | 34 | empty |
| 2 | 293 | 0.55 | 0.76 | 34 | empty |
| 3 | 250 | 0.55 | 0.77 | 36 | empty |
| 4 | 268 | 0.54 | 0.76 | 37 | empty |
| 5 | 247 | 0.54 | 0.77 | 37 | empty |
Interfaces
20 interfaces between chains.
- E–F · 3393 Ų buried · 44 hydrogen bonds · protein-protein
- I–J · 3375 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3366 Ų buried · 48 hydrogen bonds · protein-protein
- G–H · 3359 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 3303 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (oxidation).
Compared structures
- 2NVL · Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y9L0 · AlphaFold monomer V2.0 prediction for peroxiredoxin (Q9Y9L0) · a predicted model of the same protein · chain C 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 2NVL · PDBe 2NVL · UniProt Q9Y9L0
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