MolNFT v1 · #102060 · protein
Crystal structure of maize cytokinin OXIDASE/DEHYDROGENASE 4 (ZMCKO4) in complex with phenylurea inhibitor cppu in alternative spacegroup
4OAL · Cytokinin dehydrogenase 4: “Crystal structure of maize cytokinin OXIDASE/DEHYDROGENASE 4 (ZMCKO4) in complex with phenylurea inhibitor…”. X-ray diffraction, 2 ligands (FAD, 245), 12 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4OAL
- Type
- protein
- Length
- 888 residues
- Chains
- 2
- 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, 245
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytokinin dehydrogenase 4 (EC 1.5.99.12) | protein | 444 | 34% helix, 24% strand | E3T1W8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 245 · 1-(2-chloropyridin-4-yl)-3-phenylurea · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.83 | 0.86 | 78 | FAD, 245 |
| 2 | 659 | 0.83 | 0.87 | 63 | FAD, 245 |
| 3 | 293 | 0.55 | 0.76 | 35 | empty |
| 4 | 184 | 0.48 | 0.76 | 33 | DMS |
| 5 | 115 | 0.43 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 351 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 4OAL · 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 4OAL · PDBe 4OAL · UniProt E3T1W8
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