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- PDB-7qx1: ATAD2 in complex with FragLite7 -

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Basic information

Entry
Database: PDB / ID: 7qx1
TitleATAD2 in complex with FragLite7
ComponentsATPase family AAA domain-containing protein 2
KeywordsTRANSCRIPTION / ATAD2 / INHIBITOR / FRAGMENT / BROMODOMAIN / FRAGLITE
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
4-iodanyl-3~{H}-pyridin-2-one / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsTurberville, S. / Martin, M.P. / Hope, I. / Noble, M.E.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKC57659/A27310 United Kingdom
Cancer Research UKC1362/A20263 United Kingdom
Cancer Research UKC2215/A21421 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
DepositionJan 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 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 2.0Jan 11, 2023Group: Advisory / Atomic model / Database references
Category: atom_site / citation_author / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _citation_author.identifier_ORCID / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,43311
Polymers15,4541
Non-polymers98010
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area8360 Å2
Unit cell
Length a, b, c (Å)79.599, 79.599, 137.348
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-1210-

SO4

21AAA-1314-

HOH

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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 / Fragment: bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Cell (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, adenosinetriphosphatase

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Non-polymers , 5 types, 171 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-HHQ / 4-iodanyl-3~{H}-pyridin-2-one


Mass: 220.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4INO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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 / pH: 6.5 / Details: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate / PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.49→68.93 Å / Num. obs: 42789 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.022 / Rrim(I) all: 0.072 / Net I/σ(I): 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.16-68.9316.70.0463400.9990.0150.049
1.49-1.528.42.50520840.5461.2472.815

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAI

3dai


Resolution: 1.49→68.93 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.521 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.066
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2424 2188 5.123 %
Rwork0.2046 40524 -
all0.207 --
obs-42712 99.932 %
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: 34.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.685 Å2-0.342 Å2-0 Å2
2---0.685 Å20 Å2
3---2.221 Å2
Refinement stepCycle: LAST / Resolution: 1.49→68.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 47 161 1292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171082
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.6631545
X-RAY DIFFRACTIONr_angle_other_deg1.511.5882501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7965131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98321.21674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25915210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0191513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021258
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02249
X-RAY DIFFRACTIONr_nbd_refined0.2240.2280
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21045
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2574
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2107
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.340.210
X-RAY DIFFRACTIONr_nbd_other0.2830.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2650.220
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1040.21
X-RAY DIFFRACTIONr_mcbond_it2.8993.025524
X-RAY DIFFRACTIONr_mcbond_other2.8943.017523
X-RAY DIFFRACTIONr_mcangle_it3.9794.516655
X-RAY DIFFRACTIONr_mcangle_other3.9824.525656
X-RAY DIFFRACTIONr_scbond_it7.9263.907626
X-RAY DIFFRACTIONr_scbond_other7.9443.871623
X-RAY DIFFRACTIONr_scangle_it11.2355.613890
X-RAY DIFFRACTIONr_scangle_other11.2655.555885
X-RAY DIFFRACTIONr_lrange_it16.62840.4391389
X-RAY DIFFRACTIONr_lrange_other16.62240.4641390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.5290.3521540.3692953X-RAY DIFFRACTION99.8714
1.529-1.5710.3211580.3392854X-RAY DIFFRACTION100
1.571-1.6160.2811590.312768X-RAY DIFFRACTION100
1.616-1.6660.3281380.2742734X-RAY DIFFRACTION100
1.666-1.720.2721540.2562615X-RAY DIFFRACTION99.9639
1.72-1.7810.2491360.2512541X-RAY DIFFRACTION100
1.781-1.8480.2581370.2322472X-RAY DIFFRACTION100
1.848-1.9230.2421310.2272359X-RAY DIFFRACTION100
1.923-2.0090.1941180.2142298X-RAY DIFFRACTION99.9586
2.009-2.1070.2751250.2122187X-RAY DIFFRACTION100
2.107-2.2210.2261110.2012095X-RAY DIFFRACTION100
2.221-2.3560.206980.1971985X-RAY DIFFRACTION100
2.356-2.5180.232870.1921887X-RAY DIFFRACTION100
2.518-2.720.2211040.1881739X-RAY DIFFRACTION100
2.72-2.9790.251790.1951635X-RAY DIFFRACTION100
2.979-3.3310.204900.1871478X-RAY DIFFRACTION100
3.331-3.8460.226670.1751324X-RAY DIFFRACTION99.9282
3.846-4.7090.244620.1721137X-RAY DIFFRACTION100
4.709-6.6560.279470.213914X-RAY DIFFRACTION100
6.656-68.930.267330.224549X-RAY DIFFRACTION98.8115

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