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- PDB-6fuk: Crystal structure of UTX complexed with 5-carboxy-8-hydroxyquinoline -

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Basic information

Entry
Database: PDB / ID: 6fuk
TitleCrystal structure of UTX complexed with 5-carboxy-8-hydroxyquinoline
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 / MLL3/4 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / 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 ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / 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 / regulation of gene expression / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / Tetratricopeptide repeat / Tetratricopeptide repeat ...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 / Tetratricopeptide repeat / Tetratricopeptide repeat / Cupin / 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
8-hydroxyquinoline-5-carboxylic acid / : / DI(HYDROXYETHYL)ETHER / Lysine-specific demethylase 6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 ...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_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 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0989
Polymers60,2641
Non-polymers8348
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-20 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.417, 83.261, 92.898
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 , 7 types, 277 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-8XQ / 8-hydroxyquinoline-5-carboxylic acid


Mass: 189.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7NO3
#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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


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


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
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: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2→46.449 Å / Num. obs: 42377 / % possible obs: 98.3 % / Redundancy: 3.7 % / Net I/σ(I): 12.58
Reflection shellResolution: 2→5.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.67 / Num. unique obs: 6776 / % possible all: 98.4

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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: 2→46.449 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.76
RfactorNum. reflection% reflection
Rfree0.2283 2104 4.99 %
Rwork0.1863 --
obs0.1884 42158 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→46.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 48 269 4082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093950
X-RAY DIFFRACTIONf_angle_d0.8065370
X-RAY DIFFRACTIONf_dihedral_angle_d12.82338
X-RAY DIFFRACTIONf_chiral_restr0.054587
X-RAY DIFFRACTIONf_plane_restr0.006685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.35541390.35142650X-RAY DIFFRACTION99
2.0465-2.09770.37091400.31992645X-RAY DIFFRACTION99
2.0977-2.15440.29581410.27162694X-RAY DIFFRACTION100
2.1544-2.21780.29451380.25192625X-RAY DIFFRACTION99
2.2178-2.28940.27751380.22152629X-RAY DIFFRACTION98
2.2894-2.37120.25171410.20492667X-RAY DIFFRACTION100
2.3712-2.46620.24481420.20632695X-RAY DIFFRACTION100
2.4662-2.57840.26321400.20222672X-RAY DIFFRACTION99
2.5784-2.71430.27811400.20312666X-RAY DIFFRACTION99
2.7143-2.88440.25841400.20082663X-RAY DIFFRACTION98
2.8844-3.1070.23381400.20592663X-RAY DIFFRACTION98
3.107-3.41960.25931390.19562620X-RAY DIFFRACTION96
3.4196-3.91420.23141410.17132675X-RAY DIFFRACTION98
3.9142-4.93060.17491410.14222700X-RAY DIFFRACTION97
4.9306-46.46150.18921440.16912790X-RAY DIFFRACTION96

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