Research workbench
Complex STRUCTURE OF A NOVEL VIRULENCE REGULATION FACTOR SghR with its effector sucrose
Analyse Complex STRUCTURE OF A NOVEL VIRULENCE REGULATION FACTOR SghR with its effector… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CDX
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.103
- Source
- Agrobacterium tumefaciens A6
- Molecule
- LacI-type transcription factor
- UniProt
- A0A2I4PGE9
- Ligands
- GLC, FRU
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.103 · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LacI-type transcription factor | protein | 272 | 39% helix, 21% strand | A0A2I4PGE9 |
| B | LacI-type transcription factor | protein | 272 | 41% helix, 21% strand | A0A2I4PGE9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.80 | 0.88 | 51 | GLC, FRU |
| 2 | 542 | 0.80 | 0.86 | 68 | GLC, FRU |
| 3 | 255 | 0.58 | 0.78 | 40 | empty |
| 4 | 149 | 0.51 | 0.79 | 23 | empty |
| 5 | 70 | 0.43 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1402 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7CDX · Complex structure of a novel virulence regulation factor sghr with its effector sucrose · 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 A0A2I4PGE9
- Elsewhere: RCSB PDB 7CDX · PDBe 7CDX · UniProt A0A2I4PGE9
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