Research workbench
(S)-4-amino-5-phenoxypentanoate as a selective agonist of the transcription factor gabr
Analyse (S)-4-amino-5-phenoxypentanoate as a selective agonist of the transcription… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UXZ
- Type
- protein
- Length
- 717 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
- QL4, SO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Hth-type transcriptional regulatory protein gabr | protein | 358 | 43% helix, 17% strand | P94426 |
| C | Hth-type transcriptional regulatory protein gabr | protein | 359 | 44% helix, 17% strand | P94426 |
Ligands and binding sites
- QL4 · (4S)-4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methylidene)amino]-5-phenoxypentanoic acid · ligand · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 6 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.82 | 0.97 | 37 | empty |
| 2 | 218 | 0.78 | 0.92 | 35 | QL4 |
| 3 | 227 | 0.72 | 0.88 | 42 | QL4 |
| 4 | 141 | 0.52 | 0.80 | 35 | empty |
| 5 | 150 | 0.52 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- B–C · 2137 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6UXZ · (S)-4-Amino-5-phenoxypentanoate as a Selective Agonist of the Transcription Factor GabR · the same entry in another collection · chain C against C, 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 C 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 6UXZ · PDBe 6UXZ · UniProt P94426
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.