MolNFT v1 · #118033 · protein
Histidine kinase domain from the lov-hk blue-light receptor from brucella abortus
5EPV · Blue-light-activated histidine kinase: “Histidine kinase domain from the lov-hk blue-light receptor from brucella abortus”. X-ray diffraction, 2 ligands (ACP, MG), 7 pockets (best druggability 0.82). MolNFT v1 #118033 on GenesisL1…
- PDB
- 5EPV
- Type
- protein
- Length
- 750 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
- ACP, MG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 216 | 50% helix, 20% strand | Q2YKK7 |
| B | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 197 | 50% helix, 22% strand | Q2YKK7 |
| C | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 171 | 43% helix, 25% strand | Q2YKK7 |
| D | Blue-light-activated histidine kinase (EC 2.7.13.3) | protein | 166 | 45% helix, 27% strand | Q2YKK7 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.82 | 0.83 | 99 | empty |
| 2 | 298 | 0.69 | 0.84 | 41 | ACP, MG |
| 3 | 248 | 0.61 | 0.80 | 39 | ACP |
| 4 | 214 | 0.59 | 0.80 | 29 | ACP |
| 5 | 212 | 0.56 | 0.79 | 34 | ACP, MG |
Interfaces
5 interfaces between chains.
- C–D · 1903 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1394 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 499 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 383 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EPV · Histidine kinase domain from the LOV-HK blue-light receptor from Brucella abortus · 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 B against A, TM-score 0.96
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 5EPV · PDBe 5EPV · UniProt Q2YKK7
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