Research workbench
Lov domain from erythrobacter litoralis EL346 blue-light activated histidine kinase
Analyse Lov domain from erythrobacter litoralis EL346 blue-light activated histidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R38
- Type
- protein
- Length
- 432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blue-light-activated histidine kinase 2
- EC
- 2.7.13.3
- UniProt
- Q2NB77
- Ligands
- RBF
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blue-light-activated histidine kinase 2 (EC 2.7.13.3) | protein | 109 | 25% helix, 35% strand | Q2NB77 |
| B | Blue-light-activated histidine kinase 2 (EC 2.7.13.3) | protein | 107 | 26% helix, 35% strand | Q2NB77 |
| C, D | Blue-light-activated histidine kinase 2 (EC 2.7.13.3) | protein | 108 | 25% helix, 33% strand | Q2NB77 |
Ligands and binding sites
- RBF · Riboflavin · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.83 | 0.83 | 72 | empty |
| 2 | 180 | 0.78 | 0.93 | 25 | RBF |
| 3 | 162 | 0.76 | 0.92 | 24 | RBF |
| 4 | 173 | 0.75 | 0.92 | 27 | RBF |
| 5 | 165 | 0.75 | 0.91 | 24 | RBF |
Interfaces
6 interfaces between chains.
- A–C · 730 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 661 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 631 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 534 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 97 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4R38 · LOV domain from Erythrobacter litoralis EL346 blue-light activated histidine kinase · 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 B against A, TM-score 0.95
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 4R38 · PDBe 4R38 · UniProt Q2NB77
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