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- PDB-5a7n: Crystal structure of human JMJD2A in complex with compound 43 -

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Basic information

Entry
Database: PDB / ID: 5a7n
TitleCrystal structure of human JMJD2A in complex with compound 43
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE / JMJD2A / KDM4A
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin / ubiquitin protein ligase binding / positive regulation of gene expression / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain ...: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-VAO / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsNowak, R. / Velupillai, S. / Krojer, T. / Gileadi, C. / Johansson, C. / Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. ...Nowak, R. / Velupillai, 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. / Williams, E. / Riesebos, E. / 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. / ...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.
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
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)90,00017
Polymers88,6532
Non-polymers1,34815
Water5,278293
1
A: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,09310
Polymers44,3261
Non-polymers7679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9077
Polymers44,3261
Non-polymers5816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.120, 149.760, 57.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2046-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 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, 308 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-VAO / 2-(5-cyano-2-oxidanyl-phenyl)pyridine-4-carboxylic acid


Mass: 240.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8N2O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.76 % / Description: NONE
Crystal growpH: 7.5
Details: 22% PEG3350 -- 0.1M BIS-TRIS PH 7.5 -- 0.25M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.39→54 Å / Num. obs: 35446 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 39.96 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.3
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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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: 2.39→53.996 Å / SU ML: 0.36 / σ(F): 1.36 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1489 4.2 %
Rwork0.1828 --
obs0.1855 35393 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→53.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5587 0 78 293 5958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085850
X-RAY DIFFRACTIONf_angle_d1.0847942
X-RAY DIFFRACTIONf_dihedral_angle_d13.5152118
X-RAY DIFFRACTIONf_chiral_restr0.043820
X-RAY DIFFRACTIONf_plane_restr0.0051050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3901-2.46720.3241220.24213056X-RAY DIFFRACTION100
2.4672-2.55540.30891030.24783075X-RAY DIFFRACTION100
2.5554-2.65770.37711310.24653052X-RAY DIFFRACTION100
2.6577-2.77860.33181310.23943077X-RAY DIFFRACTION100
2.7786-2.92510.30581280.23023062X-RAY DIFFRACTION100
2.9251-3.10840.2821450.20523052X-RAY DIFFRACTION100
3.1084-3.34830.2621230.20323001X-RAY DIFFRACTION97
3.3483-3.68520.26921510.18593067X-RAY DIFFRACTION100
3.6852-4.21830.2211470.15733124X-RAY DIFFRACTION100
4.2183-5.31390.1661510.13283118X-RAY DIFFRACTION99
5.3139-54.010.21231570.15673220X-RAY DIFFRACTION98

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