Research workbench
Structure of the oligomerization domain of the arginine repressor from bacillus stearothermophilus
Analyse Structure of the oligomerization domain of the arginine repressor from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B4B
- Type
- protein
- Length
- 213 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine repressor
- UniProt
- O31408
- Ligands
- ARG
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginine repressor | protein | 71 | 38% helix, 35% strand | O31408 |
Ligands and binding sites
- ARG · Arginine · ligand · 3 copies · chains A, C, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.44 | 0.82 | 19 | empty |
| 2 | 70 | 0.40 | 0.80 | 15 | empty |
| 3 | 70 | 0.37 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 493 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 444 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1B4B · Structure of the oligomerization domain of the arginine repressor from bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- O31408 · AlphaFold monomer V2.0 prediction for arginine repressor (O31408) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O31408
- Elsewhere: RCSB PDB 1B4B · PDBe 1B4B · UniProt O31408
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