Research workbench
Peroxiredoxin from aeropyrum pernix K1 (apprx) 0CYS mutant
Analyse Peroxiredoxin from aeropyrum pernix K1 (apprx) 0CYS mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KRK
- Type
- protein
- Length
- 2,440 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin
- EC
- 1.11.1.15
- UniProt
- Q9Y9L0
- Pockets
- 20 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Peroxiredoxin (EC 1.11.1.15) | protein | 244 | 34% helix, 23% strand | Q9Y9L0 |
Ligands and binding sites
- CIT · Citric acid · additive · 10 copies · chains A, B, J, D, C, H, E, F, G, I
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 | 325 | 0.58 | 0.76 | 41 | CIT |
| 2 | 281 | 0.56 | 0.77 | 46 | CIT |
| 3 | 292 | 0.56 | 0.76 | 48 | CIT |
| 4 | 296 | 0.56 | 0.76 | 41 | CIT |
| 5 | 281 | 0.56 | 0.76 | 42 | CIT |
Interfaces
20 interfaces between chains.
- G–H · 3619 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3599 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3579 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 3549 Ų buried · 57 hydrogen bonds · protein-protein
- I–J · 3544 Ų buried · 55 hydrogen bonds · protein-protein
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 6KRK · PDBe 6KRK · UniProt Q9Y9L0
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