Research workbench
The crystal structure of perr-ox highlights 2-oxo-histidine formation
Analyse The crystal structure of perr-ox highlights 2-oxo-histidine formation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RGV
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxide operon regulator
- UniProt
- P71086
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxide operon regulator | protein | 141 | 46% helix, 21% strand | P71086 |
| B | Peroxide operon regulator | protein | 143 | 43% helix, 21% strand | P71086 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.54 | 0.78 | 24 | empty |
| 2 | 259 | 0.54 | 0.76 | 29 | empty |
| 3 | 50 | 0.26 | 0.73 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1728 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 2RGV · The crystal structure of PerR-Ox highlights 2-oxo-Histidine formation · the same entry in another collection · chain A against A, TM-score 1.00
- P71086 · AlphaFold monomer V2.0 prediction for peroxide operon regulator (P71086) · a predicted model of the same protein · chain A against A, TM-score 0.62
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 P71086
- Elsewhere: RCSB PDB 2RGV · PDBe 2RGV · UniProt P71086
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