5X6Z

Crystal structure of Rice Dwarf Virus P5 in complex with GTP and GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of the capping enzyme P5 from Rice Dwarf Virus

Nakamichi, Y.Higashiura, A.Narita, H.Hagiwara, K.Uehara-Ichiki, T.Omura, T.Nakagawa, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA capping enzyme P5
C, A, D, B
804Rice dwarf virus (isolate Akita)Mutation(s): 0 
Find proteins for P14583 (Rice dwarf virus (isolate Akita))
Go to UniProtKB:  P14583
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B, C, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, B, C, D
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 77.394α = 103.10
b = 83.447β = 101.98
c = 141.979γ = 95.69
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapanJP25251009

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release