Research workbench
Crystal structure of the ligand-binding domain of a putative gntr- family transcriptional regulator from bordetella bronchiseptica
Analyse Crystal structure of the ligand-binding domain of a putative gntr- family… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CNV
- Type
- protein
- Length
- 634 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative gntr-family transcriptional regulator
- UniProt
- Q7WD95
- Ligands
- CL
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative gntr-family transcriptional regulator | protein | 156 | 19% helix, 47% strand | Q7WD95 |
| B | Putative gntr-family transcriptional regulator | protein | 159 | 18% helix, 47% strand | Q7WD95 |
| C | Putative gntr-family transcriptional regulator | protein | 162 | 17% helix, 46% strand | Q7WD95 |
| D | Putative gntr-family transcriptional regulator | protein | 157 | 18% helix, 47% strand | Q7WD95 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.67 | 0.85 | 59 | CL |
| 2 | 422 | 0.66 | 0.79 | 40 | empty |
| 3 | 160 | 0.65 | 0.86 | 41 | empty |
| 4 | 361 | 0.64 | 0.79 | 36 | empty |
| 5 | 96 | 0.64 | 0.89 | 26 | FLC |
Interfaces
6 interfaces between chains.
- A–B · 1163 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1161 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 802 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 752 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 394 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3CNV · Crystal structure of the ligand-binding domain of a putative GntR-family transcriptional… · 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 Q7WD95
- Elsewhere: RCSB PDB 3CNV · PDBe 3CNV · UniProt Q7WD95
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