5GP0

Crystal structure of geraniol-NUDX1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis.

Liu, J.Guan, Z.Liu, H.Qi, L.Zhang, D.Zou, T.Yin, P.

(2018) Mol Plant 11: 218-221


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nudix hydrolase 1
A, E, F, I
149Arabidopsis thalianaMutation(s): 0 
Gene Names: NUDT1NUDX1At1g68760F14K14.13
EC: 3.6.1.55 (PDB Primary Data), 3.6.1.67 (PDB Primary Data), 3.6.1.22 (PDB Primary Data)
Find proteins for Q9CA40 (Arabidopsis thaliana)
Go to UniProtKB:  Q9CA40
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GPP
Query on GPP

Download CCD File 
A, E, F, I
GERANYL DIPHOSPHATE
C10 H20 O7 P2
GVVPGTZRZFNKDS-JXMROGBWSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
E, I
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.761α = 90
b = 83.582β = 90
c = 116.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
XDSdata processing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Database references