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- PDB-6etu: Crystal structure of KDM4D with tetrazolhydrazide compound 7 -

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Basic information

Entry
Database: PDB / ID: 6etu
TitleCrystal structure of KDM4D with tetrazolhydrazide compound 7
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / KDM4D / ligand binding / Tetrazolylhydrazide / 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-BWZ / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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 / refine_hist / 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.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 / _refine_hist.d_res_high / _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)40,28612
Polymers39,4921
Non-polymers79411
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-27 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.999, 71.999, 150.872
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-846-

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: 39491.793 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, 489 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#8: Chemical ChemComp-BWZ / [[3-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]carbonylamino]azanium


Mass: 205.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9N6O
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
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: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2016
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.33→48.239 Å / Num. obs: 174441 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.806 % / Biso Wilson estimate: 12.98 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.059 / Χ2: 1.123 / Net I/σ(I): 20.06 / Num. measured all: 1187218
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
1.33-1.416.340.7332.4217781528283280480.7710.79999.2
1.41-1.516.9820.4783.9818565926593265920.9070.517100
1.51-1.636.9170.2746.8817128724769247620.9650.296100
1.63-1.786.620.15611.2815049122737227340.9880.169100
1.78-1.997.0670.09219.5814502320635205200.9960.199.4
1.99-2.36.8040.05431.4912287418132180590.9980.05899.6
2.3-2.816.8460.03544.5410492015328153250.9990.038100
2.81-3.977.0540.02563.5283634118641185610.02799.9
3.97-48.2396.9540.02175.16455156550654510.02299.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ETS

6ets


Resolution: 1.33→48.239 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 14.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.154 2117 1.21 %RANDOM
Rwork0.1231 172311 --
obs0.1235 174428 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.07 Å2 / Biso mean: 21.0938 Å2 / Biso min: 6.95 Å2
Refinement stepCycle: final / Resolution: 1.33→48.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 83 496 3266
Biso mean--31.94 36.3 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0273218
X-RAY DIFFRACTIONf_angle_d2.264426
X-RAY DIFFRACTIONf_chiral_restr0.152446
X-RAY DIFFRACTIONf_plane_restr0.014589
X-RAY DIFFRACTIONf_dihedral_angle_d14.4721275
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 (%)
1.328-1.35880.24461360.2128113191145598
1.3588-1.39280.22331400.19141149011630100
1.3928-1.43050.18411420.16491149311635100
1.4305-1.47260.1891450.15391153511680100
1.4726-1.52010.18471370.1381154011677100
1.5201-1.57450.17891420.12161148711629100
1.5745-1.63750.13361430.10941153711680100
1.6375-1.7120.11841420.10521152511667100
1.712-1.80230.13731410.10161149211633100
1.8023-1.91520.12431370.11151145611593100
1.9152-2.06310.16611400.1145114871162799
2.0631-2.27070.14321390.1187114101154999
2.2707-2.59930.13741440.11411153011674100
2.5993-3.27470.13641440.11961151411658100
3.2747-48.27040.16841450.12421149611641100

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