MolNFT v1 · #59417 · protein
Crystal structure of effector binding domain of central glycolytic gene regulator (cggr) from bacillus subtilis in complex with dihydroxyacetone phosphate
3BXE: “Crystal structure of effector binding domain of central glycolytic gene regulator (cggr) from bacillus…”. X-ray diffraction, 1 ligand (13P), 4 pockets (best druggability 0.70). MolNFT v1 #59417 on GenesisL1: 3D structure, binding…
- PDB
- 3BXE
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Central glycolytic gene regulator
- UniProt
- O32253
- Ligands
- 13P
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Central glycolytic gene regulator | protein | 248 | 45% helix, 19% strand | O32253 |
| B | Central glycolytic gene regulator | protein | 253 | 46% helix, 19% strand | O32253 |
Ligands and binding sites
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.70 | 0.78 | 56 | empty |
| 2 | 406 | 0.69 | 0.81 | 43 | empty |
| 3 | 133 | 0.64 | 0.87 | 37 | 13P |
| 4 | 133 | 0.63 | 0.87 | 36 | 13P |
Interfaces
1 interface between chains.
- A–B · 647 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3BXE · 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 3BXE · PDBe 3BXE · UniProt O32253
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