RCSB PDB - 8HX4: Crystal structure of AtHPPD-Y18549 complex

 8HX4

Crystal structure of AtHPPD-Y18549 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NQXClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Crystal structure of AtHPPD-Y18549 complex

Dong, J.Lin, H.-Y.Yang, G.-F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxyphenylpyruvate dioxygenase417Arabidopsis thalianaMutation(s): 0 
Gene Names: HPDPDS1At1g06570F12K11.9
EC: 1.13.11.27
UniProt
Find proteins for P93836 (Arabidopsis thaliana)
Explore P93836 
Go to UniProtKB:  P93836
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93836
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NQX
Query on NQX

Download Ideal Coordinates CCD File 
C [auth A]6-[(R)-[(2R,6R)-2,6-bis(oxidanyl)cyclohexyl]-oxidanyl-methyl]-3-(4,6-dimethylpyrimidin-2-yl)-1,5-dimethyl-quinazoline-2,4-dione
C23 H28 N4 O5
MLZUNIVRBBBYRG-HLIPFELVSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
B [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.645α = 90
b = 83.528β = 100.32
c = 62.002γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NQXClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant 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: 2024-10-23
    Changes: Structure summary