MolNFT v1 · #26813 · protein
Thioredoxin peroxidase from aeropyrum pernix K1
1X0R · Probable peroxiredoxin: “Thioredoxin peroxidase from aeropyrum pernix K1”. X-ray diffraction, 19 pockets (best druggability 0.57). MolNFT v1 #26813 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1X0R
- Type
- protein
- Length
- 2,440 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
- 19 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Probable peroxiredoxin (EC 1.11.1.15) | protein | 244 | 36% helix, 24% strand | Q9Y9L0 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 128 copies · chains A, B, I, C, J, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.57 | 0.77 | 44 | EDO |
| 2 | 306 | 0.56 | 0.76 | 42 | EDO |
| 3 | 312 | 0.56 | 0.76 | 43 | EDO |
| 4 | 277 | 0.55 | 0.76 | 41 | EDO |
| 5 | 245 | 0.55 | 0.77 | 41 | EDO |
Interfaces
20 interfaces between chains.
- E–F · 3596 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 3556 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3552 Ų buried · 60 hydrogen bonds · protein-protein
- G–H · 3528 Ų buried · 53 hydrogen bonds · protein-protein
- I–J · 3504 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
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 1X0R · PDBe 1X0R · UniProt Q9Y9L0
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