Research workbench
Histidine kinase domain from Erythrobacter litoralis EL346 blue-light activated histidine kinase
Analyse Histidine kinase domain from Erythrobacter litoralis EL346 blue-light activated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R39
- Type
- protein
- Length
- 843 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.603
- Source
- Erythrobacter litoralis HTCC2594
- Molecule
- Blue-light-activated histidine kinase 2
- EC
- 2.7.13.3
- UniProt
- Q2NB77
- Ligands
- ANP, MG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.603 · 3 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Blue-light-activated histidine kinase 2 (EC 2.7.13.3) | protein | 217 | 50% helix, 18% strand | Q2NB77 |
| B | Blue-light-activated histidine kinase 2 (EC 2.7.13.3) | protein | 205 | 51% helix, 21% strand | Q2NB77 |
| C | Blue-light-activated histidine kinase 2 (EC 2.7.13.3) | protein | 204 | 53% helix, 20% strand | Q2NB77 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.79 | 0.95 | 44 | empty |
| 2 | 419 | 0.64 | 0.78 | 61 | empty |
| 3 | 414 | 0.63 | 0.77 | 56 | empty |
| 4 | 164 | 0.58 | 0.82 | 30 | MG, ANP |
| 5 | 176 | 0.58 | 0.82 | 26 | MG, ANP |
Interfaces
6 interfaces between chains.
- C–D · 1105 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1091 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1016 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 975 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 196 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4R39 · Histidine kinase domain from erythrobacter litoralis EL346 blue-light activated histidine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2NB77 · AlphaFold monomer V2.0 prediction for blue-light-activated histidine kinase 2 (Q2NB77) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 Q2NB77
- Elsewhere: RCSB PDB 4R39 · PDBe 4R39 · UniProt Q2NB77
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