Research workbench
The structure of brlr bound to C-di-gmp
Analyse The structure of brlr bound to C-di-gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XBT
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable transcriptional regulator
- UniProt
- Q9HUT5
- Ligands
- C2E
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable transcriptional regulator | protein | 271 | 43% helix, 25% strand | Q9HUT5 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- IMD · Imidazole · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.55 | 0.82 | 40 | empty |
| 2 | 112 | 0.48 | 0.79 | 25 | IMD |
| 3 | 98 | 0.42 | 0.78 | 28 | empty |
| 4 | 89 | 0.41 | 0.78 | 25 | IMD |
| 5 | 105 | 0.35 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1715 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5XBT · The structure of BrlR bound to c-di-GMP · 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 Q9HUT5
- Elsewhere: RCSB PDB 5XBT · PDBe 5XBT · UniProt Q9HUT5
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