Research workbench
Crystal structure of the DNA-binding domain of the lysr family transcriptional regulator yfba from yersinia pestis
Analyse Crystal structure of the DNA-binding domain of the lysr family transcriptional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TRV
- Type
- protein
- Length
- 353 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysr-family transcriptional regulatory protein
- UniProt
- Q8D0G2
- Ligands
- CL, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysr-family transcriptional regulatory protein | protein | 89 | 67% helix, 2% strand | Q8D0G2 |
| B | Lysr-family transcriptional regulatory protein | protein | 86 | 72% helix, 2% strand | Q8D0G2 |
| D | Lysr-family transcriptional regulatory protein | protein | 89 | 70% helix, 2% strand | Q8D0G2 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
- GOL · Glycerol · additive · 3 copies · chains B, C, D
- FMT · Formic acid · additive · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.63 | 0.79 | 37 | CL |
| 2 | 59 | 0.28 | 0.74 | 15 | CL, GOL |
Interfaces
4 interfaces between chains.
- A–B · 1400 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1367 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 550 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 85 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 7TRV · Crystal Structure of the DNA-Binding Domain of the LysR family Transcriptional Regulator… · 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 Q8D0G2
- Elsewhere: RCSB PDB 7TRV · PDBe 7TRV · UniProt Q8D0G2
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