Research workbench
Crystal structure of effector binding domain of central glycolytic gene regulator (cggr) from bacillus subtilis in complex with effector fructose-1,6-bisphosphate
Analyse Crystal structure of effector binding domain of central glycolytic gene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BXF
- Type
- protein
- Length
- 498 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Central glycolytic gene regulator
- UniProt
- O32253
- Ligands
- FBP, 13P, CL
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Central glycolytic gene regulator | protein | 253 | 45% helix, 21% strand | O32253 |
| B | Central glycolytic gene regulator | protein | 245 | 44% helix, 20% strand | O32253 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · chains A
- 13P · 1,3-dihydroxyacetonephosphate · ligand · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.74 | 0.87 | 70 | CL, 13P |
| 2 | 364 | 0.71 | 0.83 | 48 | FBP |
| 3 | 223 | 0.57 | 0.79 | 27 | empty |
| 4 | 74 | 0.35 | 0.76 | 21 | empty |
| 5 | 71 | 0.34 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 804 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3BXF · Crystal structure of effector binding domain of central glycolytic gene regulator (CggR)… · the same entry in another collection · chain A against A, TM-score 1.00
- O32253 · AlphaFold monomer V2.0 prediction for central glycolytic genes regulator (O32253) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O32253
- Elsewhere: RCSB PDB 3BXF · PDBe 3BXF · UniProt O32253
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