MolNFT v1 · #160324 · protein
Lov-pas construct from the lov-hk sensory protein from brucella abortus (dark-adapted, construct 15-273)
6PH3 · Blue-light-activated histidine kinase: “Lov-pas construct from the lov-hk sensory protein from brucella abortus (dark-adapted, construct 15-273)”. X-ray diffraction, 1 ligand (FMN), 10 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6PH3
- Type
- protein
- Length
- 1,009 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
- Q8YC53
- Ligands
- FMN
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 255 | 38% helix, 31% strand | Q8YC53 |
| B | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 257 | 37% helix, 30% strand | Q8YC53 |
| C | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 241 | 37% helix, 30% strand | Q8YC53 |
| D | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 256 | 38% helix, 30% strand | Q8YC53 |
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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.78 | 0.82 | 66 | FMN |
| 2 | 148 | 0.67 | 0.87 | 23 | FMN |
| 3 | 162 | 0.66 | 0.86 | 21 | FMN |
| 4 | 361 | 0.58 | 0.76 | 34 | empty |
| 5 | 335 | 0.58 | 0.76 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2981 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2956 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 149 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PH3 · LOV-PAS construct from the LOV-HK sensory protein from Brucella abortus (dark-adapted… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8YC53 · AlphaFold monomer V2.0 prediction for blue-light-activated histidine kinase (Q8YC53) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q8YC53
- Elsewhere: RCSB PDB 6PH3 · PDBe 6PH3 · UniProt Q8YC53
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