Research workbench
Structure of maize cytokinin OXIDASE/DEHYDROGENASE 2 (ZMCKO2)
Analyse Structure of maize cytokinin OXIDASE/DEHYDROGENASE 2 (ZMCKO2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ML8
- Type
- protein
- Length
- 1,942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytokinin oxidase 2
- UniProt
- Q709Q5
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytokinin oxidase 2 | protein | 488 | 34% helix, 23% strand | Q709Q5 |
| B | Cytokinin oxidase 2 | protein | 487 | 33% helix, 24% strand | Q709Q5 |
| D | Cytokinin oxidase 2 | protein | 479 | 34% helix, 25% strand | Q709Q5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.85 | 0.86 | 92 | FAD |
| 2 | 979 | 0.84 | 0.85 | 79 | FAD |
| 3 | 1068 | 0.84 | 0.85 | 91 | FAD |
| 4 | 1107 | 0.83 | 0.84 | 83 | FAD |
| 5 | 1092 | 0.82 | 0.84 | 99 | PEG |
Interfaces
3 interfaces between chains.
- A–B · 1108 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 584 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 461 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 4ML8 · Structure of maize cytokinin oxidase/dehydrogenase 2 (ZmCKO2) · 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 Q709Q5
- Elsewhere: RCSB PDB 4ML8 · PDBe 4ML8 · UniProt Q709Q5
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