8HZU | pdb_00008hzu

Crystal structure of AtHPPD-XHD complex

PDB DOI: https://doi.org/10.2210/pdb8HZU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-01-09 Released: 2023-12-20
Deposition Author(s): Dong, J., Lin, H.-Y., Yang, G.-F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.204 (Depositor), 0.207 (DCC)
R-Value Work:
0.186 (Depositor), 0.188 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of 4-Hydroxyphenylpyruvate dioxygenase inhibitors with novel pharmacophores

Yang, T.L., Dong, J., Wang, X.L., Dong, J., Lin, H.Y.

(2024) Adv Agrochem 3: 344-350

DOI: https://doi.org/10.1016/j.aac.2024.09.004

Macromolecule Content

Total Structure Weight: 46.3 kDa
Atom Count: 3,095
Modeled Residue Count: 377
Deposited Residue Count: 417
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A	417	Arabidopsis thaliana	Mutation(s): 0 Gene Names: HPD, PDS1, At1g06570, F12K11.9 EC: 1.13.11.27
UniProt
Find proteins for P93836 (Arabidopsis thaliana) Explore P93836 Go to UniProtKB: P93836
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P93836
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T9O Query on T9O Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(5R)-2-butanimidoyl-5-[(2R)-2-ethylsulfanylpropyl]-3-oxidanyl-cyclohex-2-en-1-one C₁₅ H₂₅ N O₂ S HITMLPXCKXYULH-XLMABRIASA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.204 (Depositor), 0.207 (DCC)
R-Value Work: 0.186 (Depositor), 0.188 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.033	α = 90
b = 84.151	β = 100.54
c = 62.394	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release
Version 1.1: 2024-10-09
Changes: Structure summary
Version 1.2: 2026-04-22
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.