8QVT | pdb_00008qvt

Crystal structure of Zea mays cytokinin oxidase/dehydrogenase 5 (ZmCKX5)

PDB DOI: https://doi.org/10.2210/pdb8QVT/pdb

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

Deposited: 2023-10-18 Released: 2024-10-30
Deposition Author(s): Kopecny, D., Briozzo, P.
Funding Organization(s): Agence Nationale de la Recherche (ANR), Czech Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.201 (Depositor), 0.207 (DCC)
R-Value Work:
0.181 (Depositor), 0.187 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Cytokinin Dehydrogenase in Xylem Sap Reveals A Direct Link Between Metabolism and Long-Distance Transport

Nedved, D., Motyka, V., Raimanova, I., Dobrev, P.I., Kopecny, D., Briozzo, P., Brunoni, F., Muller, K., Hoyerova, K.

To be published.

Macromolecule Content

Total Structure Weight: 120.73 kDa
Atom Count: 8,380
Modeled Residue Count: 1,015
Deposited Residue Count: 1,122
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytokinin dehydrogenase	A, B	561	Zea mays	Mutation(s): 0 Gene Names: CKX5, ZEAMMB73_Zm00001d008862 EC: 1.5.99.12
UniProt
Find proteins for E3T1X0 (Zea mays) Explore E3T1X0 Go to UniProtKB: E3T1X0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E3T1X0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B]