MolNFT v1 · #121152 · protein
Crystal structure of maize cytokinin OXIDASE/DEHYDROGENASE 4 (ZMCKO4) in complex with phenylurea inhibitor 3FMTDZ
5HMR · Cytokinin dehydrogenase 4: “Crystal structure of maize cytokinin OXIDASE/DEHYDROGENASE 4 (ZMCKO4) in complex with phenylurea inhibitor…”. X-ray diffraction, 2 ligands (FAD, FDZ), 8 pockets (best druggability 0.84). MolNFT v1 #121152…
- PDB
- 5HMR
- Type
- protein
- Length
- 447 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytokinin dehydrogenase 4
- EC
- 1.5.99.12
- UniProt
- E3T1W8
- Ligands
- FAD, FDZ
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokinin dehydrogenase 4 (EC 1.5.99.12) | protein | 447 | 33% helix, 24% strand | E3T1W8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- FDZ · 1-(1,2,3-thiadiazol-5-yl)-3-[3-(trifluoromethoxy)phenyl]urea · ligand · chains A
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 | 686 | 0.84 | 0.88 | 70 | FAD, FDZ |
| 2 | 178 | 0.51 | 0.78 | 23 | empty |
| 3 | 128 | 0.46 | 0.78 | 16 | empty |
| 4 | 76 | 0.42 | 0.80 | 18 | empty |
| 5 | 81 | 0.41 | 0.79 | 26 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 5HMR · Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (ZmCKO4) in complex with… · the same entry in another collection · 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 E3T1W8
- Elsewhere: RCSB PDB 5HMR · PDBe 5HMR · UniProt E3T1W8
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