	235,183 Structures from the PDB
	1,068,577 Computed Structure Models (CSM)

2EJR|pdb_00002ejr

LSD1-tranylcypromine complex

PDB DOI: https://doi.org/10.2210/pdb2EJR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-20 Released: 2008-01-01
Deposition Author(s): Sengoku, T.,Mimasu, S.,Umehara, T.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.245 (Depositor), 0.200 (DCC)
R-Value Work:
0.204 (Depositor), 0.200 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model:experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2007.11.066
Primary Citation of Related Structures:
2DW4,2EJR,2Z3Y,2Z5U

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.

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.

Macromolecule Content

Total Structure Weight: 74.57 kDa
Atom Count: 5,215
Modelled Residue Count: 643
Deposited Residue Count: 662
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1	A	662	Homo sapiens	Mutation(s): 0 Gene Names: KIAA0601, LSD1 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens) Explore O60341 Go to UniProtKB: O60341
PHAROS: O60341 GTEx: ENSG00000004487
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60341
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F2N Query on F2N Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[7,8-DIMETHYL-2,4-DIOXO-5-(3-PHENYLPROPANOYL)-1,3,4,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGEN DIPHOSPHATE C₃₆ H₄₃ N₉ O₁₆ P₂ ASOSNULLFLNYFZ-NEHYRMIBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.245 (Depositor), 0.200 (DCC)
R-Value Work: 0.204 (Depositor), 0.200 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.759	α = 90
b = 185.759	β = 90
c = 108.742	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-01-01

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-01-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description