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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase PRDM9
A, B
221Homo sapiensMutation(s): 0 
Gene Names: PRDM9PFM6
EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQV7 (Homo sapiens)
Explore Q9NQV7 
Go to UniProtKB:  Q9NQV7
GTEx:  ENSG00000164256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQV7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
U [auth B],
V [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
UNKNOWN ATOM OR ION
X
Modified Residues  1 Unique
IDChains TypeFormula2D 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 
  • 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 

Revision History  (Full details and data files)

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