Research workbench
Peroxiredoxin (wild type) from aeropyrum pernix K1 (reduced form)
Analyse Peroxiredoxin (wild type) from aeropyrum pernix K1 (reduced form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A5W
- Type
- protein
- Length
- 2,429 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 0.58
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable peroxiredoxin (EC 1.11.1.15) | protein | 241 | 37% helix, 24% strand | Q9Y9L0 |
| B, C, D, F, I | Probable peroxiredoxin (EC 1.11.1.15) | protein | 244 | 37% helix, 24% strand | Q9Y9L0 |
| E, G | Probable peroxiredoxin (EC 1.11.1.15) | protein | 242 | 36% helix, 24% strand | Q9Y9L0 |
| H | Probable peroxiredoxin (EC 1.11.1.15) | protein | 243 | 33% helix, 24% strand | Q9Y9L0 |
| J | Probable peroxiredoxin (EC 1.11.1.15) | protein | 241 | 36% helix, 24% strand | Q9Y9L0 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.58 | 0.78 | 39 | empty |
| 2 | 358 | 0.58 | 0.76 | 41 | empty |
| 3 | 342 | 0.57 | 0.76 | 49 | empty |
| 4 | 329 | 0.57 | 0.75 | 52 | empty |
| 5 | 328 | 0.56 | 0.75 | 45 | empty |
Interfaces
20 interfaces between chains.
- E–F · 3671 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3664 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3629 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 3620 Ų buried · 54 hydrogen bonds · protein-protein
- I–J · 3594 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 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 Q9Y9L0
- Elsewhere: RCSB PDB 3A5W · PDBe 3A5W · UniProt Q9Y9L0
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