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- PDB-6ets: Crystal structure of KDM4D with tetrazolhydrazide compound 1 -

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Basic information

Entry
Database: PDB / ID: 6ets
TitleCrystal structure of KDM4D with tetrazolhydrazide compound 1
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / KDM4D / ligand binding / tetrazolhydrazide / tetrazole / inhibitor design / cancer / epigenetics
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-I1L / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.333 Å
AuthorsMalecki, P.H. / Link, A. / Weiss, M.S. / Heinemann, U.
CitationJournal: Chemmedchem / Year: 2019
Title: Structure-Based Screening of Tetrazolylhydrazide Inhibitors versus KDM4 Histone Demethylases.
Authors: Malecki, P.H. / Ruger, N. / Roatsch, M. / Krylova, O. / Link, A. / Jung, M. / Heinemann, U. / Weiss, M.S.
History
DepositionOct 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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 / 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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,50718
Polymers39,3351
Non-polymers1,17217
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-31 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.631, 71.631, 150.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-829-

HOH

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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: 39334.598 Da / Num. of mol.: 1 / Fragment: JMJD2D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Production host: Escherichia coli BL21(DE3) (bacteria)
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 , 8 types, 476 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-I1L / [2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoylamino]azanium


Mass: 143.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N6O
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.894 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 22, 2016
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.894 Å / Relative weight: 1
ReflectionResolution: 1.33→48.014 Å / Num. obs: 168562 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.078 % / Biso Wilson estimate: 11.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.067 / Χ2: 1.019 / Net I/σ(I): 16.18 / Num. measured all: 687453
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.33-1.413.9820.7591.9210856727660272660.6130.86998.6
1.41-1.514.0180.4773.0710359826047257860.8010.54699
1.51-1.634.0350.2765.269704324252240500.9180.31699.2
1.63-1.794.0530.1638.658939922262220550.970.18799.1
1.79-24.080.08715.538110520177198770.9920.198.5
2-2.314.0880.04926.167176417764175550.9970.05698.8
2.31-2.824.1740.03436.416153015001147400.9980.03998.3
2.82-3.994.2850.02252.944800511626112020.9990.02596.4
3.99-48.0144.3840.01963.2126442640060310.9990.02194.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HOO

4hoo


Resolution: 1.333→32.034 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1559 2086 1.24 %Random selection
Rwork0.1287 166462 --
obs0.1291 168548 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.65 Å2 / Biso mean: 18.5015 Å2 / Biso min: 5.16 Å2
Refinement stepCycle: final / Resolution: 1.333→32.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 126 476 3289
Biso mean--35.52 32.5 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0353137
X-RAY DIFFRACTIONf_angle_d2.6174300
X-RAY DIFFRACTIONf_chiral_restr0.195432
X-RAY DIFFRACTIONf_plane_restr0.016568
X-RAY DIFFRACTIONf_dihedral_angle_d14.1981222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3325-1.36350.26511330.2399109951112898
1.3635-1.39760.22661410.2163112061134799
1.3976-1.43540.22131410.2029111321127399
1.4354-1.47760.20921340.1811111361127099
1.4776-1.52530.18461420.1653112071134999
1.5253-1.57980.22971390.1488111721131199
1.5798-1.64310.18431420.1319111431128599
1.6431-1.71790.1591450.1236112071135299
1.7179-1.80840.13691420.1165111221126499
1.8084-1.92170.1481390.1107110981123799
1.9217-2.07010.13941360.1069111261126298
2.0701-2.27840.15041380.1073111171125599
2.2784-2.60790.14181410.1117111451128699
2.6079-3.28520.14731400.1181109621110297
3.2852-32.04360.1281330.1243106941082795

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