Research workbench
Crystal structure of the C-terminal domain of bacillus subtilis gabr reveals a closed conformation by the binding of gamma-aminobutyric acid, inducing the transcriptional activation
Analyse Crystal structure of the C-terminal domain of bacillus subtilis gabr reveals a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X03
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulatory protein gabr
- UniProt
- P94426
- Ligands
- PLP, ABU
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulatory protein gabr | protein | 363 | 42% helix, 17% strand | P94426 |
| B | Hth-type transcriptional regulatory protein gabr | protein | 365 | 44% helix, 18% strand | P94426 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- ABU · Gamma-amino-butanoic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.83 | 0.96 | 39 | empty |
| 2 | 188 | 0.77 | 0.93 | 35 | PLP, ABU |
| 3 | 521 | 0.75 | 0.82 | 49 | PLP |
| 4 | 59 | 0.72 | 0.98 | 19 | empty |
| 5 | 104 | 0.57 | 0.85 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1971 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5X03 · Crystal structure of the C-terminal domain of Bacillus subtilis GabR reveals a closed… · the same entry in another collection · chain A against A, TM-score 1.00
- P94426 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulatory protein gabr… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P94426
- Elsewhere: RCSB PDB 5X03 · PDBe 5X03 · UniProt P94426
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