8CKQ

Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (CKO/CKX4) in complex with inhibitor 2-[(3,5-dichlorophenyl)carbamoylamino]benzamide

PDB DOI: https://doi.org/10.2210/pdb8CKQ/pdb

Classification: FLAVOPROTEIN
Organism(s): Zea mays
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-16 Released: 2024-02-28
Deposition Author(s): Kopecny, D., Briozzo, P., Morera, S.
Funding Organization(s): Czech Science Foundation, Ministry of Education, Youth and Sports of the Czech Republic

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.219
R-Value Work: 0.196
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Cytokinin oxidase/dehydrogenase inhibitors: progress toward a practice

Nisler, J., Koncitikova, R., Klimes, P., Kadlecova, A., Murvanidze, N., Kopecny, D., Werbrouck, S.P.O., de Diego, N., Havlicek, L., Briozzo, P., Morera, S., Zalabak, D., Spichal, L.

To be published.

Macromolecule Content

Total Structure Weight: 59.31 kDa
Atom Count: 3,731
Modelled Residue Count: 456
Deposited Residue Count: 541
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokinin dehydrogenase 4	A	541	Zea mays	Mutation(s): 0 Gene Names: CKX4 EC: 1.5.99.12
UniProt
Find proteins for E3T1W8 (Zea mays) Explore E3T1W8 Go to UniProtKB: E3T1W8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E3T1W8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UZX (Subject of Investigation/LOI) Query on UZX Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-[[3,5-bis(chloranyl)phenyl]carbamoylamino]benzamide C₁₄ H₁₁ Cl₂ N₃ O₂ CKNONNNNSSNDHJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.219
R-Value Work: 0.196
R-Value Observed: 0.197
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.47	α = 90
b = 79.47	β = 90
c = 203.57	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-28

Deposition Author(s):

Kopecny, D.

Briozzo, P.

Morera, S.

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	21-07661S
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	CZ.02.1.01/0.0/0.0/16_019/0000827

Revision History (Full details and data files)

Version 1.0: 2024-02-28
Type: Initial release

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8CKQ

Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (CKO/CKX4) in complex with inhibitor 2-[(3,5-dichlorophenyl)carbamoylamino]benzamide

Cytokinin oxidase/dehydrogenase inhibitors: progress toward a practice

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)