MolNFT v2 · #78215 · protein
Pro427Gln mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenine
3S1E · Cytokinin dehydrogenase 1: “Pro427Gln mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenine”. X-ray diffraction at 1.9, 3 ligands (FAD, ZIP, NAG), 4 pockets (best druggability 0.86). MolNFT v2 #78215…
- PDB
- 3S1E
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Zea mays
- Molecule
- Cytokinin dehydrogenase 1
- EC
- 1.5.99.12
- UniProt
- Q9T0N8
- Ligands
- FAD, ZIP, NAG
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokinin dehydrogenase 1 (EC 1.5.99.12) | protein | 499 | 37% helix, 23% strand | Q9T0N8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- ZIP · N-(3-methylbut-2-en-1-yl)-9H-purin-6-amine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.86 | 0.90 | 79 | FAD, ZIP |
| 2 | 323 | 0.63 | 0.79 | 30 | GOL |
| 3 | 89 | 0.44 | 0.79 | 20 | PEG |
| 4 | 85 | 0.33 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 3 glycan, 1 cofactor (N-glycosylation, flavinylation).
Compared structures
- 3S1E · PRO427GLN mutant of maize cytokinin OXIDASE/DEHYDROGENASE complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9T0N8 · AlphaFold monomer V2.0 prediction for cytokinin dehydrogenase 1 (Q9T0N8) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9T0N8
- Elsewhere: RCSB PDB 3S1E · PDBe 3S1E · UniProt Q9T0N8
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