2VYT

The MBT repeats of human SCML2 bind to peptides containing mono methylated lysine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Malignant Brain Tumor Repeats of Human Scml2 Bind to Peptides Containing Monomethylated Lysine.

Santiveri, C.M.Lechtenberg, B.C.Allen, M.D.Sathyamurthy, A.Jaulent, A.M.Freund, S.M.V.Bycroft, M.

(2008) J Mol Biol 382: 1107

  • DOI: 10.1016/j.jmb.2008.07.081
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • SCML2 (sex comb on midleg-like 2) is a constituent of the Polycomb repressive complex 1, a large multiprotein assembly required for the repression of developmental control genes. It contains two MBT (malignant brain tumor) repeats; the MBT is a prote ...

    SCML2 (sex comb on midleg-like 2) is a constituent of the Polycomb repressive complex 1, a large multiprotein assembly required for the repression of developmental control genes. It contains two MBT (malignant brain tumor) repeats; the MBT is a protein module structurally similar to domains that bind to methylated histones. We have used NMR spectroscopy to examine the binding specificity of these repeats. Our data show that they preferentially bind histone peptides monomethylated at lysine residues with no apparent sequence specificity. The crystal structure of the complex between the protein and monomethyllysine reveals that the modified amino acid binds to an aromatic rich pocket at one end of the beta-barrel of the second repeat.


    Organizational Affiliation

    MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SEX COMB ON MIDLEG-LIKE PROTEIN 2A, B221Homo sapiensMutation(s): 1 
Gene Names: SCML2
Find proteins for Q9UQR0 (Homo sapiens)
Explore Q9UQR0 
Go to UniProtKB:  Q9UQR0
NIH Common Fund Data Resources
PHAROS  Q9UQR0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLZ
Query on MLZ

Download CCD File 
A, B
N-METHYL-LYSINE
C7 H16 N2 O2
PQNASZJZHFPQLE-LURJTMIESA-N
 Ligand Interaction
PGE
Query on PGE

Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MLZKd:  1840000   nM  Binding MOAD
MLZKd :  1840000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.53α = 90
b = 99.21β = 90
c = 131.277γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy