6DBZ

Crystal structure of Nudix 1 from Arabidopsis thaliana complexed with isopentenyl diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Contribution of isopentenyl phosphate to plant terpenoid metabolism.

Henry, L.K.Thomas, S.T.Widhalm, J.R.Lynch, J.H.Davis, T.C.Kessler, S.A.Bohlmann, J.Noel, J.P.Dudareva, N.

(2018) Nat Plants 4: 721-729


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nudix hydrolase 1
A, B
150Arabidopsis thalianaMutation(s): 0 
Gene Names: NUDT1 (NUDX1)
Find proteins for Q9CA40 (Arabidopsis thaliana)
Go to Gene View: NUDT1
Go to UniProtKB:  Q9CA40
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPR
Query on IPR

Download SDF File 
Download CCD File 
A, B
ISOPENTYL PYROPHOSPHATE
C5 H14 O7 P2
IPFXNYPSBSIFOB-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.050α = 90.00
b = 72.751β = 90.00
c = 116.390γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
Aimlessdata scaling
BOSdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesEEC-0813570

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release