Research workbench
Corynebacterium glutamicum oxyr C206S mutant, H2O2-bound
Analyse Corynebacterium glutamicum oxyr C206S mutant, H2O2-bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G4R
- Type
- protein
- Length
- 1,235 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogen peroxide-inducible genes activator
- UniProt
- A0A2H5I9R9
- Ligands
- PEO, SO4
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Hydrogen peroxide-inducible genes activator | protein | 322 | 44% helix, 20% strand | A0A2H5I9R9 |
| A | Hydrogen peroxide-inducible genes activator | protein | 310 | 39% helix, 21% strand | A0A2H5I9R9 |
| E | Hydrogen peroxide-inducible genes activator | protein | 310 | 44% helix, 20% strand | A0A2H5I9R9 |
| G | Hydrogen peroxide-inducible genes activator | protein | 293 | 41% helix, 22% strand | A0A2H5I9R9 |
Ligands and binding sites
- PEO · Hydrogen peroxide · ligand · 3 copies · chains B, E
- SO4 · Sulfate ion · ion · chains B, E
- EDO · 1,2-ethanediol · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.84 | 0.85 | 111 | empty |
| 2 | 802 | 0.78 | 0.82 | 81 | SO4 |
| 3 | 294 | 0.74 | 0.87 | 46 | empty |
| 4 | 203 | 0.53 | 0.78 | 36 | empty |
| 5 | 177 | 0.44 | 0.74 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–E · 1583 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1506 Ų buried · 27 hydrogen bonds · protein-protein
- A–G · 1331 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 1235 Ų buried · 21 hydrogen bonds · protein-protein
- B–A · 823 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (oxidation).
Compared structures
- 6G4R · Corynebacterium glutamicum OxyR C206S mutant, H2O2-bound · the same entry in another collection · chain B against B, 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 A0A2H5I9R9
- Elsewhere: RCSB PDB 6G4R · PDBe 6G4R · UniProt A0A2H5I9R9
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