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- PDB-6ful: Crystal structure of UTX complexed with 5-hydroxy-4-keto-1-methyl... -

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Basic information

Entry
Database: PDB / ID: 6ful
TitleCrystal structure of UTX complexed with 5-hydroxy-4-keto-1-methyl-picolinate
ComponentsLysine-specific demethylase 6A
KeywordsOXIDOREDUCTASE / Jumonji Demethylase / Inhibitor
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / chromatin DNA binding ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / chromatin DNA binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / heart development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / regulation of gene expression / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Cupin ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Cupin / Tetratricopeptide repeat / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribbon / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-E7Z / : / Lysine-specific demethylase 6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 Å
AuthorsEsposito, C. / Sledz, P. / Caflisch, A.
CitationJournal: J Chem Inf Model / Year: 2018
Title: In Silico Identification of JMJD3 Demethylase Inhibitors.
Authors: Esposito, C. / Wiedmer, L. / Caflisch, A.
History
DepositionFeb 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,25011
Polymers60,2641
Non-polymers98610
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-74 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.181, 82.801, 93.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 6A / Histone demethylase UTX / Ubiquitously-transcribed TPR protein on the X chromosome / Ubiquitously- ...Histone demethylase UTX / Ubiquitously-transcribed TPR protein on the X chromosome / Ubiquitously-transcribed X chromosome tetratricopeptide repeat protein


Mass: 60264.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM6A, UTX / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O15550, 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, 637 molecules

#2: Chemical ChemComp-E7Z / 1-methyl-5-oxidanyl-4-oxidanylidene-pyridine-2-carboxylic acid


Mass: 169.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 51.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), Li2 SO4 (0.15-0.25 M), PEG 3350 (20-25% w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.649→48.761 Å / Num. obs: 138199 / % possible obs: 96.9 % / Redundancy: 1.96 % / Net I/σ(I): 8.02
Reflection shellResolution: 1.649→4.92 Å / Redundancy: 1.9 % / Num. unique obs: 22076 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AVS

3avs


Resolution: 1.649→48.761 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 22.97
RfactorNum. reflection% reflection
Rfree0.2079 6862 4.97 %
Rwork0.1764 --
obs0.1779 138111 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.649→48.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 52 627 4477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074045
X-RAY DIFFRACTIONf_angle_d0.8035513
X-RAY DIFFRACTIONf_dihedral_angle_d3.9553289
X-RAY DIFFRACTIONf_chiral_restr0.054596
X-RAY DIFFRACTIONf_plane_restr0.006710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6491-1.66790.35532150.33764051X-RAY DIFFRACTION89
1.6679-1.68750.3282300.30454477X-RAY DIFFRACTION98
1.6875-1.70810.32542220.29224379X-RAY DIFFRACTION98
1.7081-1.72970.26962330.28274401X-RAY DIFFRACTION97
1.7297-1.75250.28772250.26994326X-RAY DIFFRACTION96
1.7525-1.77650.30552260.25864324X-RAY DIFFRACTION96
1.7765-1.80190.28792320.24464360X-RAY DIFFRACTION96
1.8019-1.82880.25722220.23924290X-RAY DIFFRACTION95
1.8288-1.85730.28252300.2344365X-RAY DIFFRACTION97
1.8573-1.88780.27022300.22294374X-RAY DIFFRACTION97
1.8878-1.92030.23612320.20844408X-RAY DIFFRACTION98
1.9203-1.95530.2282370.20074446X-RAY DIFFRACTION99
1.9553-1.99290.23882370.19694493X-RAY DIFFRACTION99
1.9929-2.03350.22082310.18954470X-RAY DIFFRACTION99
2.0335-2.07780.2292370.18844509X-RAY DIFFRACTION99
2.0778-2.12610.2082300.18074446X-RAY DIFFRACTION99
2.1261-2.17930.2372290.18094396X-RAY DIFFRACTION98
2.1793-2.23820.21632300.1764449X-RAY DIFFRACTION98
2.2382-2.3040.23122290.1794379X-RAY DIFFRACTION97
2.304-2.37840.22442260.17754369X-RAY DIFFRACTION97
2.3784-2.46340.24672170.17534221X-RAY DIFFRACTION94
2.4634-2.5620.20912310.18444260X-RAY DIFFRACTION95
2.562-2.67860.23632250.18164342X-RAY DIFFRACTION96
2.6786-2.81980.20962290.17124388X-RAY DIFFRACTION97
2.8198-2.99650.19932400.16864425X-RAY DIFFRACTION98
2.9965-3.22780.19642320.174437X-RAY DIFFRACTION98
3.2278-3.55250.18912300.15854419X-RAY DIFFRACTION98
3.5525-4.06640.17292250.14464399X-RAY DIFFRACTION97
4.0664-5.12230.16362160.13184235X-RAY DIFFRACTION94
5.1223-48.78210.1732340.17184411X-RAY DIFFRACTION98

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