3DQ0 | pdb_00003dq0

Maize cytokinin oxidase/dehydrogenase complexed with N6-(3-methoxy-phenyl)adenine

• PDB DOI: https://doi.org/10.2210/pdb3DQ0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zea mays
• Expression System: Yarrowia lipolytica
• Mutation(s): No 


• Deposited: 2008-07-09 Released: 2009-07-14 
• Deposition Author(s): Kopecny, D., Briozzo, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.237 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.204 (Depositor) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Characterization and biological activity of novel purine-derived inhibitor of cytokinin oxidase/dehydrogenase and its potential use for in vivo studies

Spichal, L., Werner, T., Galuszka, P., Zatloukal, T., Kopecny, D., Briozzo, P., Nisler, J., Gruz, J., Frebortova, J., Schmulling, T., Strnad, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.9 kDa 
• Atom Count: 4,391 
• Modeled Residue Count: 498 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokinin dehydrogenase 1	A	516	Zea mays	Mutation(s): 0  Gene Names: CKX1 EC: 1.5.99.12
UniProt
Find proteins for Q9T0N8 (Zea mays) Explore Q9T0N8  Go to UniProtKB:  Q9T0N8
Glycosylation
Glycosylation Sites: 5

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	G [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MZO	H [auth A]	N-(3-methoxyphenyl)-9H-purin-6-amine C12 H11 N5 O AXPCHVXFDHPTBW-UHFFFAOYSA-N
NAG	D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.237 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.204 (Depositor) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 252.7	α = 90
b = 50.4	β = 93.7
c = 51	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Kopecny, D., Briozzo, P.

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary