4IJD

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

Structural Biology Knowledgebase: 4IJD SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IJD

Classification: TRANSFERASE

Total Structure Weight: 50951.52

Macromolecule Entities
Molecule Chains Length Organism Details
Histone-lysine N-methyltransferase PRDM9 A, B 221 Homo sapiens EC#: 2.1.1.43 IUBMB
Fragment: UNP residues 195-415
Gene Name(s): PRDM9 Gene View PFM6

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A, B UNKNOWN ATOM OR ION
X
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

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 = 54.73 α = 90.00
b = 48.78 β = 100.05
c = 78.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-21
  • Released Date: 2013-02-13
  • Deposition author(s): Dong, A., Dombrovski, L., Li, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Wu, H., Structural Genomics Consortium (SGC)

Revision History

No revisions since initial release