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- PDB-5a7q: Crystal structure of human JMJD2A in complex with compound 30 -

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Basic information

Entry
Database: PDB / ID: 5a7q
TitleCrystal structure of human JMJD2A in complex with compound 30
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE / JMJD2A / KDM4A
Function / homology
Function and homology information


HDMs demethylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / histone demethylation / histone H3-K36 demethylation / histone demethylase activity (H3-K36 specific) / histone demethylase activity (H3-K9 specific) / histone H3-K9 demethylation / histone demethylase activity / Oxidoreductases, Acting on paired donors, with incorporation or reduction of molecular oxygen, With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / methylated histone binding ...HDMs demethylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / histone demethylation / histone H3-K36 demethylation / histone demethylase activity (H3-K36 specific) / histone demethylase activity (H3-K9 specific) / histone H3-K9 demethylation / histone demethylase activity / Oxidoreductases, Acting on paired donors, with incorporation or reduction of molecular oxygen, With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / methylated histone binding / histone methyltransferase complex / negative regulation of autophagy / fibrillar center / chromatin remodeling / negative regulation of gene expression / negative regulation of transcription, DNA-templated / viral process / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Tudor domain / JmjC domain, hydroxylase / Zinc finger, PHD-type / JmjN domain / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Extended PHD (ePHD) domain / JmjC domain / Lysine-specific demethylase 4, Tudor domain / jmjN domain ...Tudor domain / JmjC domain, hydroxylase / Zinc finger, PHD-type / JmjN domain / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Extended PHD (ePHD) domain / JmjC domain / Lysine-specific demethylase 4, Tudor domain / jmjN domain / Jumonji domain-containing protein 2A Tudor domain / JmjN domain profile. / JmjC domain profile. / Extended PHD (ePHD) domain profile.
Lysine-specific demethylase 4A
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVelupillai, S. / Krojer, T. / Gileadi, C. / Johansson, C. / Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. / Iwasa, E. / Pollock, S.B. / Ortiz Torres, I. / Kopec, J. / Dixon-Clarke, S. / MacKenzie, A. / Nowak, R. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Shoichet, B.K. / Fujimori, D.G. / Oppermann, U.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors.
Authors: Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. / Krojer, T. / Velupillai, S. / Gileadi, C. / Nowak, R.P. / Iwasa, E. / Pollock, S.B. / Ortiz Torres, I. / Oppermann, U. / Shoichet, B.K. / Fujimori, D.G.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSINE-SPECIFIC DEMETHYLASE 4A
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,63214
Polymers88,6532
Non-polymers97912
Water5,927329
1
A: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8037
Polymers44,3261
Non-polymers4766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8297
Polymers44,3261
Non-polymers5036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)101.194, 149.080, 57.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide LYSINE-SPECIFIC DEMETHYLASE 4A / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A / JUMONJI DOMAIN-CONTAINING PROTEIN 2A


Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75164, Oxidoreductases, Acting on paired donors, with incorporation or reduction of molecular oxygen, With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Non-polymers , 6 types, 341 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Manganese
#3: Chemical ChemComp-KCH / 2-(5-azanyl-2-oxidanyl-phenyl)pyridine-4-carboxylic acid


Mass: 230.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10N2O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Zinc
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Chloride
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Ethylene glycol
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.5
Details: 28% PEG3350 -- 0.1M BIS-TRIS PH 6.5 -- 0.15M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→149.08 Å / Num. obs: 59779 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OQ7
Resolution: 2→83.7271 Å / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 2947 4.9 %
Rwork0.1938 --
Obs-56771 0.999 %
Refinement stepCycle: LAST / Resolution: 2→83.7271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5638 0 47 329 6014

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