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- PDB-7ppx: ATAD2 in complex with FragLite3 -

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Basic information

Entry
Database: PDB / ID: 7ppx
TitleATAD2 in complex with FragLite3
ComponentsATPase family AAA domain-containing protein 2
KeywordsTRANSCRIPTION / Transcription regulation / Activator / Hydrolase / Nucleotide-binding / Fragment binding / inhibitor
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 / bromo domain / Bromodomain ...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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
4-bromanyl-1,2-oxazole / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsTurberville, S. / Martin, M.P. / Hope, I. / Wood, D.J. / Ng, Y.M. / Heath, R. / Endicott, J.A. / Noble, M.E.M.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N009738/1 United Kingdom
Cancer Research UKC2215/A21421 United Kingdom
Cancer Research UKC57659/A27310 United Kingdom
Cancer Research UKC1362/A20263 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions.
Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / ...Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / Endicott, J.A. / Hardcastle, I.R. / Noble, M.E.M. / Waring, M.J.
History
DepositionSep 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 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 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 11, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Jan 31, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,57417
Polymers15,4541
Non-polymers1,12016
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint5 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.205, 79.205, 137.910
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
11AAA-1216-

SO4

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Components

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Protein , 1 types, 1 molecules AAA

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


Mass: 15453.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pET 28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLyS / References: UniProt: Q6PL18, EC: 3.6.1.3

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Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-7ZX / 4-bromanyl-1,2-oxazole


Mass: 147.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2BrNO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH 7.0, 2.4 AmSO4, ATAD2~5 mg mL-1.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97959 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.35→68.96 Å / Num. obs: 56615 / % possible obs: 99.7 % / Redundancy: 19.8 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.017 / Rrim(I) all: 0.058 / Net I/σ(I): 22.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.39-68.96160.0314380.9980.010.033
1.35-1.3710.33.926670.2041.8134.317
7.39-68.96160.0314380.9980.010.033
1.35-1.3710.33.926670.2041.8134.317

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
pointlessdata scaling
DIALSdata collection
DIMPLEphasing
Cootmodel building
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAI

3dai


Resolution: 1.35→68.688 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.216 / Average fsc free: 0.8859 / Average fsc work: 0.8913 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2306 2936 5.193 %
Rwork0.2108 53598 -
all0.212 --
obs-56534 99.607 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.546 Å2
Baniso -1Baniso -2Baniso -3
1-0.024 Å20.012 Å20 Å2
2--0.024 Å2-0 Å2
3----0.077 Å2
Refinement stepCycle: LAST / Resolution: 1.35→68.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 65 163 1312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0121187
X-RAY DIFFRACTIONr_angle_refined_deg2.2471.6741585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5585137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23520.92176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03815215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9191514
X-RAY DIFFRACTIONr_chiral_restr0.1370.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02903
X-RAY DIFFRACTIONr_nbd_refined0.2270.2583
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2801
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2135
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2340.220
X-RAY DIFFRACTIONr_mcbond_it2.8172.575539
X-RAY DIFFRACTIONr_mcangle_it3.9923.833679
X-RAY DIFFRACTIONr_scbond_it5.7613.315648
X-RAY DIFFRACTIONr_scangle_it8.3564.69906
X-RAY DIFFRACTIONr_lrange_it11.50538.6831888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.3431890.3423784X-RAY DIFFRACTION96.432
1.385-1.4230.322060.3273755X-RAY DIFFRACTION98.8027
1.423-1.4640.332020.3013721X-RAY DIFFRACTION100
1.464-1.5090.3242030.2733595X-RAY DIFFRACTION100
1.509-1.5590.2741810.273512X-RAY DIFFRACTION100
1.559-1.6130.2672020.2513369X-RAY DIFFRACTION100
1.613-1.6740.2561770.2433276X-RAY DIFFRACTION100
1.674-1.7430.251580.2343163X-RAY DIFFRACTION100
1.743-1.820.241700.2413036X-RAY DIFFRACTION100
1.82-1.9090.2851560.2352917X-RAY DIFFRACTION99.9675
1.909-2.0120.2591370.2252785X-RAY DIFFRACTION100
2.012-2.1340.2671530.2242625X-RAY DIFFRACTION100
2.134-2.2820.2371540.2082470X-RAY DIFFRACTION100
2.282-2.4640.2261320.2072324X-RAY DIFFRACTION100
2.464-2.70.2131190.1972147X-RAY DIFFRACTION100
2.7-3.0180.1881040.2011959X-RAY DIFFRACTION100
3.018-3.4850.211090.181740X-RAY DIFFRACTION100
3.485-4.2670.185850.1551500X-RAY DIFFRACTION100
4.267-6.0320.214600.1871203X-RAY DIFFRACTION100
6.032-68.6880.243390.271717X-RAY DIFFRACTION97.6744

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