MolNFT v1 · #79481 · protein
Arabidopsis histidine kinase 4 sensor domain in complex with N- isopentenyl adenine
3T4J: “Arabidopsis histidine kinase 4 sensor domain in complex with N- isopentenyl adenine”. X-ray diffraction, 1 ligand (ZIP), 8 pockets (best druggability 0.74). MolNFT v1 #79481 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3T4J
- Type
- protein
- Length
- 528 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
- ZIP
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% 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 | 266 | 42% helix, 26% strand | Q9C5U0 |
| B | Histidine kinase 4 (EC 2.7.13.3, 3.1.3.16) | protein | 262 | 42% helix, 27% strand | Q9C5U0 |
Ligands and binding sites
- ZIP · N-(3-methylbut-2-en-1-yl)-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 | 114 | 0.74 | 0.94 | 29 | ZIP |
| 2 | 122 | 0.73 | 0.93 | 33 | ZIP |
| 3 | 119 | 0.40 | 0.75 | 17 | empty |
| 4 | 98 | 0.39 | 0.76 | 16 | MLI |
| 5 | 89 | 0.37 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1029 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3T4J · Arabidopsis histidine kinase 4 sensor domain in complex with N-isopentenyl adenine · 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 3T4J · PDBe 3T4J · UniProt Q9C5U0
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