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 
  • R-Value Observed: 0.199 

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 PRDM9A, B221Homo sapiensMutation(s): 0 
Gene Names: PRDM9PFM6
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt), 2.1.1.359 (UniProt), 2.1.1.354 (UniProt), 2.1.1.355 (UniProt), 2.1.1.362 (UniProt), 2.1.1.361 (UniProt)
Find proteins for Q9NQV7 (Homo sapiens)
Explore Q9NQV7 
Go to UniProtKB:  Q9NQV7
NIH Common Fund Data Resources
PHAROS  Q9NQV7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-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 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.734α = 90
b = 48.782β = 100.05
c = 78.713γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data scaling
SOLVEphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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