Research workbench
A blue light illuminated lov-pas construct from the lov-hk sensory protein from brucella abortus (construct 15-273)
Analyse A blue light illuminated lov-pas construct from the lov-hk sensory protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PPS
- Type
- protein
- Length
- 1,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blue-light-activated histidine kinase
- EC
- 2.7.13.3
- UniProt
- Q2YKK7
- Ligands
- FMN
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 255 | 34% helix, 30% strand | Q2YKK7 |
| B | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 257 | 36% helix, 30% strand | Q2YKK7 |
| C | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 256 | 32% helix, 28% strand | Q2YKK7 |
| D | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 259 | 37% helix, 31% strand | Q2YKK7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.77 | 0.82 | 60 | FMN |
| 2 | 92 | 0.75 | 0.96 | 20 | empty |
| 3 | 54 | 0.71 | 0.98 | 16 | empty |
| 4 | 166 | 0.67 | 0.87 | 23 | FMN |
| 5 | 146 | 0.66 | 0.87 | 23 | FMN |
Interfaces
3 interfaces between chains.
- C–D · 2895 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2829 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 123 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PPS · A blue light illuminated LOV-PAS construct from the LOV-HK sensory protein from Brucella… · the same entry in another collection · chain D against D, TM-score 1.00
- Q2YKK7 · AlphaFold monomer V2.0 prediction for blue-light-activated histidine kinase (Q2YKK7) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q2YKK7
- Elsewhere: RCSB PDB 6PPS · PDBe 6PPS · UniProt Q2YKK7
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