[English] 日本語
Yorodumi
- PDB-6kgr: LSD1-FCPA-MPE N5 adduct model -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kgr
TitleLSD1-FCPA-MPE N5 adduct model
ComponentsLysine-specific histone demethylase 1A
KeywordsOXIDOREDUCTASE / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / MECHANISM-BASED INHIBITOR
Function / homology
Function and homology information


guanine metabolic process / : / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation ...guanine metabolic process / : / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / regulation of androgen receptor signaling pathway / MRF binding / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of stem cell proliferation / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of cell size / histone demethylase activity / positive regulation of epithelial to mesenchymal transition / response to fungicide / cellular response to cAMP / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / nuclear receptor coactivator activity / positive regulation of protein ubiquitination / negative regulation of protein binding / Regulation of PTEN gene transcription / HDACs deacetylate histones / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of DNA-binding transcription factor activity / HDMs demethylate histones / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / cellular response to UV / p53 binding / flavin adenine dinucleotide binding / positive regulation of cold-induced thermogenesis / regulation of protein localization / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Histone lysine-specific demethylase / ATP synthase, gamma subunit, helix hairpin domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / : / Amine oxidase / Flavin containing amine oxidoreductase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily ...Histone lysine-specific demethylase / ATP synthase, gamma subunit, helix hairpin domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / : / Amine oxidase / Flavin containing amine oxidoreductase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DJC / FLAVIN-ADENINE DINUCLEOTIDE / Lysine-specific histone demethylase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsNiwa, H. / Sato, S. / Handa, N. / Umehara, T.
CitationJournal: Chemmedchem / Year: 2020
Title: Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors.
Authors: Niwa, H. / Sato, S. / Handa, N. / Sengoku, T. / Umehara, T. / Yokoyama, S.
History
DepositionJul 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific histone demethylase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5334
Polymers74,3331
Non-polymers1,2003
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-20 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.268, 185.268, 109.327
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-1260-

HOH

21A-1261-

HOH

-
Components

#1: Protein Lysine-specific histone demethylase 1A / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2


Mass: 74333.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Plasmid: PETDUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: O60341, Oxidoreductases
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-DJC / 3-[4-[5-fluoranyl-2-(trifluoromethyl)phenyl]phenyl]propanal


Mass: 296.259 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H12F4O
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer details6KGQ and 6KGR use the same data but have ligand models with possible different configurations.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES (pH 7.5), 5% MPD, 3.5-4.0% PEG MME 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→48.04 Å / Num. obs: 48179 / % possible obs: 100 % / Redundancy: 18.4 % / Biso Wilson estimate: 48.35 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.091 / Rsym value: 0.098 / Net I/σ(I): 24.4
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 18.2 % / Mean I/σ(I) obs: 3 / Num. unique obs: 4362 / CC1/2: 0.896 / Rpim(I) all: 0.315 / Rrim(I) all: 1.363 / Rsym value: 1.326 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→34.88 Å / SU ML: 0.2482 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 22.0271
RfactorNum. reflection% reflection
Rfree0.1983 4559 5.02 %
Rwork0.1682 --
obs0.1698 48129 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.02 Å2
Refinement stepCycle: LAST / Resolution: 2.32→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 82 164 5340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745288
X-RAY DIFFRACTIONf_angle_d0.87477183
X-RAY DIFFRACTIONf_chiral_restr0.0501804
X-RAY DIFFRACTIONf_plane_restr0.0063969
X-RAY DIFFRACTIONf_dihedral_angle_d13.06223203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.32171460.28742878X-RAY DIFFRACTION99.87
2.35-2.370.28571650.26842884X-RAY DIFFRACTION99.93
2.37-2.40.29581670.24842843X-RAY DIFFRACTION100
2.4-2.430.26931440.24012876X-RAY DIFFRACTION100
2.43-2.470.2451420.22552881X-RAY DIFFRACTION99.97
2.47-2.50.25651680.2182886X-RAY DIFFRACTION99.93
2.5-2.530.27111430.21732892X-RAY DIFFRACTION99.97
2.53-2.570.26021150.21392887X-RAY DIFFRACTION99.93
2.57-2.610.20791590.21872857X-RAY DIFFRACTION99.97
2.61-2.660.24461880.21282879X-RAY DIFFRACTION99.84
2.66-2.70.2481270.19612858X-RAY DIFFRACTION100
2.7-2.750.23351380.20432879X-RAY DIFFRACTION99.93
2.75-2.80.27451060.2082957X-RAY DIFFRACTION100
2.8-2.860.21951450.19922866X-RAY DIFFRACTION100
2.86-2.920.26251450.20182880X-RAY DIFFRACTION100
2.92-2.990.21241490.2092908X-RAY DIFFRACTION100
2.99-3.070.24561460.20362857X-RAY DIFFRACTION100
3.07-3.150.25851570.19732872X-RAY DIFFRACTION100
3.15-3.240.21241920.18542837X-RAY DIFFRACTION100
3.24-3.350.24951370.1842891X-RAY DIFFRACTION100
3.35-3.460.24361450.17772889X-RAY DIFFRACTION100
3.46-3.60.20231640.17012852X-RAY DIFFRACTION100
3.6-3.770.18191510.15732913X-RAY DIFFRACTION100
3.77-3.970.15531540.14442853X-RAY DIFFRACTION100
3.97-4.210.1881760.13612868X-RAY DIFFRACTION100
4.21-4.540.14651840.13162838X-RAY DIFFRACTION100
4.54-4.990.16951600.13222875X-RAY DIFFRACTION100
4.99-5.710.15331830.14932842X-RAY DIFFRACTION100
5.71-7.190.19131450.16212885X-RAY DIFFRACTION100
7.19-34.880.14751180.1282902X-RAY DIFFRACTION99.37
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.483764386491.618202987110.6389873995693.216664538760.2188886815510.9718432305930.0458595378111-0.2387139408570.0948090810603-0.0675303178848-0.0467191619801-0.330080505499-0.1536928809620.161418244687-0.005561302547160.381246840194-0.01883251073340.03170456707440.419806786364-0.06622429838340.3029077196344.128558742-38.366263248622.0941881843
20.878367948052-1.34610074457-1.238642371465.748333533135.988879558046.662775336790.0433296341650.243500432384-0.448756427078-0.09017876543780.0179112011168-0.06509478725220.4640574000290.304022401849-0.03934059004160.7532445692750.1004000828590.03484959845910.630600195935-0.1529087733270.69246618449635.4189557238-82.5636829985-30.6653527868
31.582471660770.2745498352370.08877934508682.793705216890.7410154075961.90391071740.0904036987144-0.1765678958190.0651071285086-0.175579882602-0.06342218466950.0272831030543-0.085531256154-0.165055934308-0.02868991658940.259120335267-0.0003991259387450.003488096939740.348293942421-0.001488323673250.24377780041125.2023901314-47.076073602314.5431700113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 172 through 371 )
2X-RAY DIFFRACTION2chain 'A' and (resid 372 through 513 )
3X-RAY DIFFRACTION3chain 'A' and (resid 514 through 832 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more