Research workbench
Huge conformation shift of vibrio cholerae vqma dimer in the absence of target DNA provides insight into DNA-binding mechanisms of luxr- type receptors
Analyse Huge conformation shift of vibrio cholerae vqma dimer in the absence of target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KJU
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Helix-turn-helix transcriptional regulator
- UniProt
- A0A0F0AZW0
- Ligands
- A1U
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Helix-turn-helix transcriptional regulator | protein | 221 | 45% helix, 25% strand | A0A0F0AZW0 |
| B | Helix-turn-helix transcriptional regulator | protein | 227 | 42% helix, 23% strand | A0A0F0AZW0 |
Ligands and binding sites
- A1U · 3,5-dimethylpyrazin-2-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.60 | 0.83 | 26 | empty |
| 2 | 304 | 0.58 | 0.77 | 31 | empty |
| 3 | 139 | 0.52 | 0.80 | 25 | empty |
| 4 | 149 | 0.48 | 0.77 | 24 | empty |
| 5 | 131 | 0.41 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2631 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6KJU · Huge conformation shift of Vibrio cholerae VqmA dimer in the absence of target DNA… · the same entry in another collection · chain A against A, 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 A0A0F0AZW0
- Elsewhere: RCSB PDB 6KJU · PDBe 6KJU · UniProt A0A0F0AZW0
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