4C1Q

Crystal structure of the PRDM9 SET domain in complex with H3K4me2 and AdoHcy.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 4C1Q

Classification: TRANSFERASE / PEPTIDE

Total Structure Weight: 41658.86

Macromolecule Entities
Molecule Chains Length Organism Details
HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9 A, B 175 Mus musculus EC#: 2.1.1.43 IUBMB
Fragment: SET DOMAIN, RESIDUES 198-368
Gene Name(s): Prdm9 Hst1 Meisetz
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HISTONE H3.1 C 10 Homo sapiens Fragment: N-TERMINUS, RESIDUES 2-11
Mutation: S10Y
Details: DOUBLE METHYLATION ON LYSINE 4
Gene Name(s): HIST1H3A Gene View H3FA HIST1H3B Gene View H3FL HIST1H3C Gene View H3FC HIST1H3D Gene View H3FB HIST1H3E Gene View H3FD HIST1H3F Gene View H3FI HIST1H3G Gene View H3FH HIST1H3H Gene View H3FK HIST1H3I Gene View H3FF HIST1H3J Gene View H3FJ
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)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MLY
Query on MLY
C L-PEPTIDE LINKING C8 H18 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.208
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 55.73 α = 90.00
b = 78.18 β = 90.00
c = 107.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-08-13
  • Released Date: 2013-10-16
  • Deposition author(s): Mathioudakis, N., Cusack, S., Kadlec, J.

Revision History

  • 2013-11-06
    Type: Database references