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Crystal structure of peroxiredoxin-1
Analyse Crystal structure of peroxiredoxin-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E4U
- Type
- protein
- Length
- 1,722 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin 1
- UniProt
- G0T332
- Ligands
- CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Peroxiredoxin 1 | protein | 176 | 28% helix, 26% strand | G0T332 |
| B | Peroxiredoxin 1 | protein | 170 | 29% helix, 26% strand | G0T332 |
| C, D, G, I, J | Peroxiredoxin 1 | protein | 171 | 30% helix, 26% strand | G0T332 |
| E | Peroxiredoxin 1 | protein | 172 | 29% helix, 26% strand | G0T332 |
| H | Peroxiredoxin 1 | protein | 173 | 28% helix, 26% strand | G0T332 |
Ligands and binding sites
- CA · Calcium ion · metal · 11 copies · chains A, B, D, C, E, F, I
- GOL · Glycerol · additive · 7 copies · chains C, F, E, G
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 | 1133 | 0.76 | 0.78 | 98 | CA |
| 2 | 68 | 0.74 | 0.98 | 23 | empty |
| 3 | 52 | 0.72 | 0.99 | 21 | empty |
| 4 | 57 | 0.72 | 0.98 | 22 | empty |
| 5 | 52 | 0.71 | 0.99 | 22 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1281 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1263 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1195 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1164 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1152 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7E4U · Crystal structure of Peroxiredoxin-1 · the same entry in another collection · chain A 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 G0T332
- Elsewhere: RCSB PDB 7E4U · PDBe 7E4U · UniProt G0T332
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