MolNFT v1 · #49479 · protein
LEU492ALA mutant of maize cytokinin OXIDASE/DEHYDROGENASE complexed with benzylurea inhibitor cpbu
2QPM · Cytokinin dehydrogenase 1: “LEU492ALA mutant of maize cytokinin OXIDASE/DEHYDROGENASE complexed with benzylurea inhibitor cpbu”. X-ray diffraction, 3 ligands (FAD, 246, NAG), 3 pockets (best druggability 0.87). MolNFT v1 #49479 on…
- PDB
- 2QPM
- Type
- protein
- Length
- 496 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, 246, NAG
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokinin dehydrogenase 1 (EC 1.5.99.12) | protein | 496 | 37% helix, 22% strand | Q9T0N8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- 246 · 1-benzyl-3-(2-chloropyridin-4-yl)urea · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.87 | 0.90 | 74 | FAD, 246 |
| 2 | 320 | 0.63 | 0.80 | 31 | empty |
| 3 | 119 | 0.37 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 5 glycan, 1 cofactor (N-glycosylation, flavinylation).
Compared structures
- 2QPM · Leu492Ala mutant of Maize cytokinin oxidase/dehydrogenase complexed with benzylurea… · 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 2QPM · PDBe 2QPM · UniProt Q9T0N8
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