4IJD

Crystal structure of methyltransferase domain of human PR domain-containing protein 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of methyltransferase domain of human PR domain-containing protein 9

Dombrovski, L.Dong, A.Li, Y.Tempel, W.Bountra, C.Arrowsmith, C.H.Edwards, A.M.Brown, P.J.Wu, H.Structural Genomics Consortium (SGC)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase PRDM9
A, B
221Homo sapiensMutation(s): 0 
Gene Names: PRDM9 (PFM6)
EC: 2.1.1.43
Find proteins for Q9NQV7 (Homo sapiens)
Go to Gene View: PRDM9
Go to UniProtKB:  Q9NQV7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.734α = 90.00
b = 48.782β = 100.05
c = 78.713γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-3000data scaling
SBC-Collectdata collection
SOLVEphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description