6IRZ

Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Cap-specific terminalN6-methylation of RNA by an RNA polymerase II-associated methyltransferase.

Akichika, S.Hirano, S.Shichino, Y.Suzuki, T.Nishimasu, H.Ishitani, R.Sugita, A.Hirose, Y.Iwasaki, S.Nureki, O.Suzuki, T.

(2018) Science --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PDX1 C-terminal-inhibiting factor 1
A
496Danio rerioMutation(s): 2 
Gene Names: pcif1
Find proteins for A0A0R4IKJ1 (Danio rerio)
Go to UniProtKB:  A0A0R4IKJ1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
M7G
Query on M7G

Download SDF File 
Download CCD File 
A
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
C11 H19 N5 O11 P2
QQODJOAVWUWVHJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.669α = 90.00
b = 83.165β = 90.00
c = 93.132γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release