7X5R

Crystal structure of AtHPPD-Lancotrione complex

PDB DOI: https://doi.org/10.2210/pdb7X5R/pdb

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

Deposited: 2022-03-05 Released: 2022-06-01
Deposition Author(s): Lin, H.-Y., Dong, J., Yang, G.-F.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.206
R-Value Work: 0.174
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural insights of 4-Hydrophenylpyruvate dioxygenase inhibition by structurally diverse small molecules

Dong, J., Dong, J., Yu, X.H., Yan, Y.C., Nan, J.X., He, B., Ye, B.Q., Yang, W.C., Lin, H.Y., Yang, G.F.

(2022) Adv Agrochem

DOI: https://doi.org/10.1016/j.aac.2022.10.002

Macromolecule Content

Total Structure Weight: 46.86 kDa
Atom Count: 3,260
Modelled Residue Count: 386
Deposited Residue Count: 417
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P93836
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9P5 Query on 9P5 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]	(1R,3R)-2-[(S)-[2-chloranyl-3-[2-(1,3-dioxolan-2-yl)ethoxy]-4-methylsulfonyl-phenyl]-oxidanyl-methyl]cyclohexane-1,3-diol C₁₉ H₂₇ Cl O₈ S HSPYNMFOCRTYFY-SNUQEOBHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [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]