MolNFT v1 · #78180 · protein
Maize cytokinin OXIDASE/DEHYDROGENASE complexed with N6- isopentenyladenosine
3S1C · Cytokinin dehydrogenase 1: “Maize cytokinin OXIDASE/DEHYDROGENASE complexed with N6- isopentenyladenosine”. X-ray diffraction, 3 ligands (FAD, ZIR, NAG), 4 pockets (best druggability 0.87). MolNFT v1 #78180 on GenesisL1: 3D…
- PDB
- 3S1C
- Type
- protein
- Length
- 498 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytokinin dehydrogenase 1
- EC
- 1.5.99.12
- UniProt
- Q9T0N8
- Ligands
- FAD, ZIR, NAG
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokinin dehydrogenase 1 (EC 1.5.99.12) | protein | 498 | 38% helix, 22% strand | Q9T0N8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- ZIR · N-(3-methylbut-2-en-1-yl)adenosine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- GOL · Glycerol · additive · 14 copies · chains A
- 15P · Polyethylene glycol (N=34) · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · 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 | 793 | 0.87 | 0.90 | 81 | FAD, ZIR, GOL, 15P |
| 2 | 316 | 0.60 | 0.78 | 31 | empty |
| 3 | 81 | 0.34 | 0.75 | 15 | GOL |
| 4 | 54 | 0.31 | 0.76 | 20 | GOL |
Modifications
Observed in the structure: 3 glycan, 1 cofactor (N-glycosylation, flavinylation).
Compared structures
- 3S1C · Maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine · 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 3S1C · PDBe 3S1C · UniProt Q9T0N8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.