3ZN1

LSD1-CoREST in complex with PRLYLV peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Protein Recognition by Small Peptide Reversible Inhibitors of the Chromatin-Modifying Lsd1/Corest Lysine Demethylase.

Tortorici, M.Borrello, M.T.Tardugno, M.Chiarelli, L.R.Pilotto, S.Ciossani, G.Vellore, N.A.Bailey, S.G.Cowan, J.O'Connell, M.Crabb, S.J.Packham, G.K.Mai, A.Baron, R.Ganesan, A.Mattevi, A.

(2013) ACS Chem Biol 8: 1677

  • DOI: 10.1021/cb4001926
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The combinatorial assembly of protein complexes is at the heart of chromatin biology. Lysine demethylase LSD1(KDM1A)/CoREST beautifully exemplifies this concept. The active site of the enzyme tightly associates to the N-terminal domain of transcripti ...

    The combinatorial assembly of protein complexes is at the heart of chromatin biology. Lysine demethylase LSD1(KDM1A)/CoREST beautifully exemplifies this concept. The active site of the enzyme tightly associates to the N-terminal domain of transcription factors of the SNAIL1 family, which therefore can competitively inhibit the binding of the N-terminal tail of the histone substrate. Our enzymatic, crystallographic, spectroscopic, and computational studies reveal that LSD1/CoREST can bind to a hexapeptide derived from the SNAIL sequence through recognition of a positively charged α-helical turn that forms upon binding to the enzyme. Variations in sequence and length of this six amino acid ligand modulate affinities enabling the same binding site to differentially interact with proteins that exert distinct biological functions. The discovered short peptide inhibitors exhibit antiproliferative activities and lay the foundation for the development of peptidomimetic small molecule inhibitors of LSD1.


    Organizational Affiliation

    Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A
A
872Homo sapiensMutation(s): 0 
Gene Names: KDM1AAOF2KDM1KIAA0601LSD1
EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
Find proteins for O60341 (Homo sapiens)
Go to UniProtKB:  O60341
NIH Common Fund Data Resources
PHAROS  O60341

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REST COREPRESSOR 1
B
482Homo sapiensMutation(s): 0 
Gene Names: RCOR1KIAA0071RCOR
Find proteins for Q9UKL0 (Homo sapiens)
Go to UniProtKB:  Q9UKL0
NIH Common Fund Data Resources
PHAROS  Q9UKL0
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE
C
6Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.23α = 90
b = 181.06β = 90
c = 232.93γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references