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- PDB-7q6v: Crystal structure of the bromodomain of ATAD2 with triazolopyridi... -

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Basic information

Entry
Database: PDB / ID: 7q6v
TitleCrystal structure of the bromodomain of ATAD2 with triazolopyridine (cpd 14)
ComponentsATPase family AAA domain-containing protein 2
KeywordsGENE REGULATION / bromodomain / epigenetics
Function / homology
Function and homology information


nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-95O / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsPatel, S.J. / Winter-Holt, J.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of a Potent and Selective ATAD2 Bromodomain Inhibitor with Antiproliferative Activity in Breast Cancer Models.
Authors: Winter-Holt, J.J. / Bardelle, C. / Chiarparin, E. / Dale, I.L. / Davey, P.R.J. / Davies, N.L. / Denz, C. / Fillery, S.M. / Guerot, C.M. / Han, F. / Hughes, S.J. / Kulkarni, M. / Liu, Z. / ...Authors: Winter-Holt, J.J. / Bardelle, C. / Chiarparin, E. / Dale, I.L. / Davey, P.R.J. / Davies, N.L. / Denz, C. / Fillery, S.M. / Guerot, C.M. / Han, F. / Hughes, S.J. / Kulkarni, M. / Liu, Z. / Milbradt, A. / Moss, T.A. / Niu, H. / Patel, J. / Rabow, A.A. / Schimpl, M. / Shi, J. / Sun, D. / Yang, D. / Guichard, S.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1045
Polymers15,4541
Non-polymers6514
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-33 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.124, 79.124, 137.997
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1203-

SO4

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Components

#1: Protein ATPase family AAA domain-containing protein 2 / AAA nuclear coregulator cancer-associated protein / ANCCA


Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold / References: UniProt: Q6PL18, adenosinetriphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-95O / (1R,9S)-13-[(8-azanyl-3-methyl-[1,2,4]triazolo[4,3-a]pyridin-6-yl)carbonyl]-11,13-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4,6-trien-10-one


Mass: 362.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.03 Å3/Da / Density % sol: 69.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.25
Details: ATAD2 (981-1108) at 12 mg/ml in 25 mM Tris pH 9.7, 300 mM NaCl, 0.5 mM TCEP crystallised from 20% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.25. Ligands were introduced by ...Details: ATAD2 (981-1108) at 12 mg/ml in 25 mM Tris pH 9.7, 300 mM NaCl, 0.5 mM TCEP crystallised from 20% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.25. Ligands were introduced by soaking, cryo-protection with 20 % glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.5406 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.96→48.62 Å / Num. obs: 18579 / % possible obs: 98 % / Redundancy: 5.4 % / Biso Wilson estimate: 27.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.03 / Rrim(I) all: 0.071 / Net I/σ(I): 19.4 / Num. measured all: 100672
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.96-2.13.20.411973230560.7850.2580.489391.1
5.55-48.625.50.02551069270.9990.0120.02853.997.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.4.8data scaling
AMoREphasing
BUSTER2.11.6refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal model

Resolution: 1.96→48.62 Å / Cor.coef. Fo:Fc: 0.9413 / Cor.coef. Fo:Fc free: 0.9367 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 939 5.06 %RANDOM
Rwork0.1871 ---
obs0.1881 18568 97.55 %-
Displacement parametersBiso max: 100.17 Å2 / Biso mean: 31.09 Å2 / Biso min: 12.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.4186 Å20 Å20 Å2
2--0.4186 Å20 Å2
3----0.8372 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: final / Resolution: 1.96→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 42 182 1308
Biso mean--37.97 43.51 -
Num. residues----130
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d431SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes165HARMONIC5
X-RAY DIFFRACTIONt_it1158HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion151SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1503SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1158HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1577HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion16.38
LS refinement shellResolution: 1.96→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2456 138 5.14 %
Rwork0.2155 2547 -
all0.217 2685 -
obs--97.55 %

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