5X6Y

Crystal structure of Rice Dwarf Virus P5 in complex with S-adenosylmethionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mRNA capping enzyme P5A, B, C, D804Rice dwarf virus (isolate O)Mutation(s): 0 
EC: 2.7.7.50
UniProt
Find proteins for P14583 (Rice dwarf virus (isolate Akita))
Explore P14583 
Go to UniProtKB:  P14583
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], K [auth B], P [auth C], Q [auth C]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
J [auth A], O [auth B], U [auth D]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , L [auth B] , M [auth B] , N [auth B] , R [auth C] , S [auth D] , 
G [auth A],  H [auth A],  I [auth A],  L [auth B],  M [auth B],  N [auth B],  R [auth C],  S [auth D],  T [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.182α = 73.8
b = 122.778β = 87.14
c = 129.257γ = 86.08
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapanJP25251009

Revision History  (Full details and data files)

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