Research workbench
Arabidopsis histidine kinase 4 sensor domain in complex with N- benzyladenine
Analyse Arabidopsis histidine kinase 4 sensor domain in complex with N- benzyladenine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T4K
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine kinase 4
- EC
- 2.7.13.3, 3.1.3.16
- UniProt
- Q9C5U0
- Ligands
- EMU
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine kinase 4 (EC 2.7.13.3, 3.1.3.16) | protein | 268 | 41% helix, 25% strand | Q9C5U0 |
| B | Histidine kinase 4 (EC 2.7.13.3, 3.1.3.16) | protein | 263 | 42% helix, 26% strand | Q9C5U0 |
Ligands and binding sites
- EMU · N-benzyl-9H-purin-6-amine · ligand · 2 copies · chains A, B
- MLI · Malonate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.75 | 0.93 | 33 | EMU |
| 2 | 134 | 0.74 | 0.93 | 33 | EMU |
| 3 | 172 | 0.47 | 0.76 | 29 | empty |
| 4 | 109 | 0.39 | 0.75 | 17 | MLI |
| 5 | 93 | 0.38 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1033 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3T4K · Arabidopsis histidine kinase 4 sensor domain in complex with N-benzyladenine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9C5U0 · AlphaFold monomer V2.0 prediction for histidine kinase 4 (Q9C5U0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9C5U0
- Elsewhere: RCSB PDB 3T4K · PDBe 3T4K · UniProt Q9C5U0
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