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- PDB-6ett: Crystal structure of KDM4D with tetrazole compound 4 -

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Basic information

Entry
Database: PDB / ID: 6ett
TitleCrystal structure of KDM4D with tetrazole compound 4
ComponentsLysine-specific demethylase 4D
KeywordsGENE REGULATION / 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 / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...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 / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / inflammatory response / chromatin remodeling / chromatin / nucleoplasm / nucleus / metal ion binding
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
ethyl 2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoate / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.257 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 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,80120
Polymers39,4921
Non-polymers1,31019
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-29 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.450, 71.450, 150.539
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: 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, 505 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.: 11 / 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-BXH / ethyl 2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoate


Mass: 156.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N4O2
#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.: 486 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
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 19, 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: 1.26→47.897 Å / Num. obs: 202280 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.288 % / Biso Wilson estimate: 11.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.067 / Χ2: 1.053 / Net I/σ(I): 16.45 / Num. measured all: 1069690
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
1.26-1.335.1460.8352.0116789932739326240.6790.92999.6
1.33-1.435.2160.5553.0416070930814308110.830.617100
1.43-1.545.2620.3265.1615041328586285850.9360.362100
1.54-1.695.3010.1848.9513988226389263890.9780.204100
1.69-1.895.3360.10515.0112701023801238010.9930.116100
1.89-2.185.3670.05626.6911283721026210260.9980.062100
2.18-2.665.3840.039389569717773177730.9990.043100
2.66-3.765.4080.02652.257425213730137300.9990.029100
3.76-47.8975.4360.02162.7740991755475410.9990.02399.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.257→27.745 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1455 2117 1.05 %RANDOM
Rwork0.1229 200134 --
obs0.1231 202251 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.63 Å2 / Biso mean: 19.0742 Å2 / Biso min: 6.79 Å2
Refinement stepCycle: final / Resolution: 1.257→27.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 158 501 3337
Biso mean--35.47 34.14 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123138
X-RAY DIFFRACTIONf_angle_d1.6084286
X-RAY DIFFRACTIONf_chiral_restr0.104427
X-RAY DIFFRACTIONf_plane_restr0.007563
X-RAY DIFFRACTIONf_dihedral_angle_d13.1571209
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 (%)
1.2574-1.28670.2511410.2327132101335199
1.2867-1.31880.21161360.20961336413500100
1.3188-1.35450.23181430.19591338713530100
1.3545-1.39430.1951470.17531334013487100
1.3943-1.43930.19911430.15731332913472100
1.4393-1.49080.14621440.13951336113505100
1.4908-1.55050.1691400.12251337213512100
1.5505-1.6210.15211420.1121331313455100
1.621-1.70650.14411380.10361337113509100
1.7065-1.81340.12421410.10511332313464100
1.8134-1.95340.12251410.10161334913490100
1.9534-2.14990.14751430.10591338313526100
2.1499-2.46080.13371380.10661334313481100
2.4608-3.09970.15091390.11461335113490100
3.0997-27.75190.11781410.12011333813479100

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