Research workbench
Peroxiredoxin from aeropyrum pernix K1 (apprx) 0CYS W211A mutant
Analyse Peroxiredoxin from aeropyrum pernix K1 (apprx) 0CYS W211A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KRS
- Type
- protein
- Length
- 2,420 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 0.66
Structure
x-ray diffraction · 1 distinct chain · 36% 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 | 242 | 36% helix, 23% strand | Q9Y9L0 |
Ligands and binding sites
- CIT · Citric acid · additive · 10 copies · chains A, B, E, H, C, D, F, I, G, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.66 | 0.91 | 18 | empty |
| 2 | 104 | 0.63 | 0.88 | 20 | empty |
| 3 | 81 | 0.59 | 0.88 | 18 | empty |
| 4 | 55 | 0.58 | 0.90 | 17 | empty |
| 5 | 109 | 0.58 | 0.85 | 23 | empty |
Interfaces
20 interfaces between chains.
- G–H · 3293 Ų buried · 44 hydrogen bonds · protein-protein
- I–J · 3279 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3239 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 3229 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3211 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 6KRS · Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W211A mutant · the same entry in another collection · chain J against J, 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 6KRS · PDBe 6KRS · UniProt Q9Y9L0
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