3S7D

Structural Basis of Substrate Methylation and Inhibition of SMYD2

Structural Biology Knowledgebase: 3S7D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.184

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3S7D

Classification: transferase

Total Structure Weight: 52075.04

Macromolecule Entities
Molecule Chains Length Organism Details
N-lysine methyltransferase SMYD2 A 433 Homo sapiens Mutation: G165E
Gene Name(s): SMYD2 Gene View KMT3C
Monomethylated p53 peptide I 13 synthetic

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BU3
Query on BU3

A (R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SAH IC50: 180 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MLZ
Query on MLZ
I L-PEPTIDE LINKING C7 H16 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.184
  • Space Group: I 4
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 153.84 α = 90.00
b = 153.84 β = 90.00
c = 52.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-26
  • Released Date: 2011-08-10
  • Deposition author(s): Ferguson, A.D.

Revision History

  • 2011-09-21
    Type: Citation | Details: Citation update