Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74235.52 
• Atom Count: 5021 
• Residue Count: 660 
• Unique protein chains: 1

2DW4

Crystal structure of human LSD1 at 2.3 A resolution

• DOI: 10.2210/pdb2DW4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2006-08-02 Released: 2007-09-04 
• Deposition Author(s): Sengoku, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 

Literature

Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25A

Mimasu, S., Sengoku, T., Fukuzawa, S., Umehara, T., Yokoyama, S.

(2008) Biochem.Biophys.Res.Commun. 366: 15-22

• PubMed: 18039463 
• DOI: 10.1016/j.bbrc.2007.11.066
• Primary Citation of Related Structures:  
  2Z5U, 2Z3Y, 2EJR


• PubMed Abstract: 
  

Transcriptional activity and chromatin structure accessibility are correlated with the methylation of specific histone residues. Lysine-specific demethylase 1 (LSD1) is the first discovered histone demethylase, which demethylates Lys4 or Lys9 of histone H3, using FAD. Among the known monoamine oxidase inhibitors, tranylcypromine (Parnate) showed the most potent inhibitory effect on LSD1. Recently, the crystal structure of LSD1 and tranylcypromine was solved at 2.75 A, revealing a five-membered ring fused to the flavin of LSD1. In this study, we refined the crystal structure of the LSD1-tranylcypromine complex to 2.25 A. The five-membered ring model did not fit completely with the electron density, giving R(work)/R(free) values of 0.226/0.254. On the other hand, the N(5) adduct gave the lowest R(work)/R(free) values of 0.218/0.248, among the tested models. These results imply that the LSD1-tranylcypromine complex is not completely composed of the five-membered adduct, but partially contains an intermediate, such as the N(5) adduct.

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Organizational Affiliation: 

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysine-specific histone demethylase 1	A	660	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A (AOF2, KDM1, KIAA0601, LSD1) EC: 1.-.-.-
Find proteins for O60341 (Homo sapiens) Go to Gene View: KDM1A Go to UniProtKB:  O60341

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FAD	A	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 184.310	α = 90.00
b = 184.310	β = 90.00
c = 108.768	γ = 120.00

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data scaling
SOLVE	phasing
HKL-2000	data reduction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-02 
• Released Date: 2007-09-04 
• Deposition Author(s): Sengoku, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2007-09-04
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance