4H12

The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 4H12

Classification: TRANSFERASE

Total Structure Weight: 32571.58

Macromolecule Entities
Molecule Chains Length Organism Details
Histone-lysine N-methyltransferase SETD2 A 278 Homo sapiens EC#: 2.1.1.43 IUBMB
Fragment: methyltransferase domain (UNP residues 1434-1711)
Gene Name(s): SETD2 Gene View HIF1 HYPB KIAA1732 KMT3A SET2 HSPC069
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.207
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 52.29 α = 90.00
b = 76.66 β = 90.00
c = 78.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-10
  • Released Date: 2012-10-03
  • Deposition author(s): Amaya, M.F., Dong, A., Zeng, H., Mackenzie, F., Bunnage, M., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)
  • This entry supercedes: 3H6L

Revision History

  • Version 1_0: 2012-10-03

    Type: Initial release

  • Version 1_1: 2012-10-24

    Type: Database references

  • Version 1_2: 2012-11-14

    Type: Database references