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- PDB-5f5a: Crystal Structure of human JMJD2D complexed with KDOAM16 -

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Basic information

Entry
Database: PDB / ID: 5f5a
TitleCrystal Structure of human JMJD2D complexed with KDOAM16
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / DOUBLE-STRANDED BETA HELIX / DEMETHYLASE / OXYGENASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of chromatin binding / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / regulation of protein phosphorylation / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination ...positive regulation of chromatin binding / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / regulation of protein phosphorylation / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-5V0 / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 Å
AuthorsKrojer, T. / Vollmar, M. / Crawley, L. / Bradley, A.R. / Szykowska, A. / Ruda, G.F. / Yang, H. / Burgess-Brown, N. / Brennan, P. / Bountra, C. ...Krojer, T. / Vollmar, M. / Crawley, L. / Bradley, A.R. / Szykowska, A. / Ruda, G.F. / Yang, H. / Burgess-Brown, N. / Brennan, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2016
Title: 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Authors: Bavetsias, V. / Lanigan, R.M. / Ruda, G.F. / Atrash, B. / McLaughlin, M.G. / Tumber, A. / Mok, N.Y. / Le Bihan, Y.V. / Dempster, S. / Boxall, K.J. / Jeganathan, F. / Hatch, S.B. / Savitsky, ...Authors: Bavetsias, V. / Lanigan, R.M. / Ruda, G.F. / Atrash, B. / McLaughlin, M.G. / Tumber, A. / Mok, N.Y. / Le Bihan, Y.V. / Dempster, S. / Boxall, K.J. / Jeganathan, F. / Hatch, S.B. / Savitsky, P. / Velupillai, S. / Krojer, T. / England, K.S. / Sejberg, J. / Thai, C. / Donovan, A. / Pal, A. / Scozzafava, G. / Bennett, J.M. / Kawamura, A. / Johansson, C. / Szykowska, A. / Gileadi, C. / Burgess-Brown, N.A. / von Delft, F. / Oppermann, U. / Walters, Z. / Shipley, J. / Raynaud, F.I. / Westaway, S.M. / Prinjha, R.K. / Fedorov, O. / Burke, R. / Schofield, C.J. / Westwood, I.M. / Bountra, C. / Muller, S. / van Montfort, R.L. / Brennan, P.E. / Blagg, J.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Structure summary
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine-specific demethylase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,56521
Polymers40,0171
Non-polymers1,54720
Water6,197344
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-24 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.280, 71.280, 150.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 4D / JmjC domain-containing histone demethylation protein 3D / Jumonji domain-containing protein 2D


Mass: 40017.348 Da / Num. of mol.: 1 / Fragment: Oxidoreductase-2OG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6B0I6, 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, 364 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-5V0 / 2-[(furan-2-ylmethylamino)methyl]pyridine-4-carboxylic acid


Mass: 232.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% PEG3350 , 0.1M HEPES pH 7.0 , 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 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.41→50.4 Å / Num. obs: 75484 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Net I/σ(I): 18.6 / Num. measured all: 986424
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
1.41-1.4512.80.7223.77025554770.9010.207
6.31-50.412.20.06740.11231310100.9990.02

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D6Q

4d6q


Resolution: 1.41→50.4 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.502 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1647 3769 5 %RANDOM
Rwork0.1311 ---
obs0.1328 71618 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.88 Å2 / Biso mean: 19.075 Å2 / Biso min: 6.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å2-0 Å2
2--0.31 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 1.41→50.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 91 344 3085
Biso mean--31.53 35.78 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193001
X-RAY DIFFRACTIONr_bond_other_d0.0020.022735
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.944076
X-RAY DIFFRACTIONr_angle_other_deg0.992.9936302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2875372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89323.706143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96215474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8311516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213492
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02754
X-RAY DIFFRACTIONr_mcbond_it1.611.5931425
X-RAY DIFFRACTIONr_mcbond_other1.611.5941426
X-RAY DIFFRACTIONr_mcangle_it2.1372.3991816
X-RAY DIFFRACTIONr_rigid_bond_restr1.73435736
X-RAY DIFFRACTIONr_sphericity_free36.7315103
X-RAY DIFFRACTIONr_sphericity_bonded9.88355891
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 289 -
Rwork0.154 5183 -
all-5472 -
obs--99.8 %

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