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- PDB-7qzy: ATAD2 in complex with FragLite29 -

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Basic information

Entry
Database: PDB / ID: 7qzy
TitleATAD2 in complex with FragLite29
ComponentsATPase family AAA domain-containing protein 2
KeywordsTRANSCRIPTION / ATAD2 / INHIBITOR / FRAGMENT / BROMODOMAIN / FRAGLITE
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / 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-bromanyl-1-(2-methoxyethyl)pyridin-2-one / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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
DepositionFeb 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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)16,34812
Polymers15,4541
Non-polymers89411
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-3 kcal/mol
Surface area8570 Å2
Unit cell
Length a, b, c (Å)79.160, 79.160, 136.456
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-1318-

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, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 129 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-V3U / 4-bromanyl-1-(2-methoxyethyl)pyridin-2-one


Mass: 232.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10BrNO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.2 %
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: 0.915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.93→68.55 Å / Num. obs: 19756 / % possible obs: 100 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.045 / Rrim(I) all: 0.149 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.05-68.5516.10.0662610.9990.020.069
1.93-1.9817.62.78412950.660.9552.945

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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: 1.93→68.55 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.098 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2453 1003 5.098 %
Rwork0.1973 18672 -
all0.2 --
obs-19675 99.853 %
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: 40.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.103 Å2-0.051 Å2-0 Å2
2---0.103 Å20 Å2
3---0.333 Å2
Refinement stepCycle: LAST / Resolution: 1.93→68.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 63 118 1265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131176
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171125
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.6741575
X-RAY DIFFRACTIONr_angle_other_deg1.4291.592599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1755131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97620.75979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36715219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3961515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
X-RAY DIFFRACTIONr_nbd_refined0.2180.2274
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21034
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2563
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3980.220
X-RAY DIFFRACTIONr_nbd_other0.2320.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2220.216
X-RAY DIFFRACTIONr_mcbond_it4.0353.731527
X-RAY DIFFRACTIONr_mcbond_other4.0393.725526
X-RAY DIFFRACTIONr_mcangle_it5.2525.55657
X-RAY DIFFRACTIONr_mcangle_other5.2485.558658
X-RAY DIFFRACTIONr_scbond_it5.6344.531647
X-RAY DIFFRACTIONr_scbond_other5.6344.531647
X-RAY DIFFRACTIONr_scangle_it8.3366.541916
X-RAY DIFFRACTIONr_scangle_other8.3316.554917
X-RAY DIFFRACTIONr_lrange_it11.89247.0921385
X-RAY DIFFRACTIONr_lrange_other11.88847.1311386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.281680.2781347X-RAY DIFFRACTION100
1.98-2.0340.232680.261310X-RAY DIFFRACTION99.9275
2.034-2.0930.292840.2411263X-RAY DIFFRACTION100
2.093-2.1580.233730.2121238X-RAY DIFFRACTION100
2.158-2.2280.264600.2021212X-RAY DIFFRACTION100
2.228-2.3070.208540.2041183X-RAY DIFFRACTION99.9192
2.307-2.3940.254560.2091141X-RAY DIFFRACTION99.9165
2.394-2.4910.257600.1981095X-RAY DIFFRACTION100
2.491-2.6020.243670.1981025X-RAY DIFFRACTION99.8172
2.602-2.7290.262490.2041030X-RAY DIFFRACTION100
2.729-2.8770.269550.201955X-RAY DIFFRACTION99.8024
2.877-3.0510.257430.2927X-RAY DIFFRACTION99.897
3.051-3.2620.265440.189860X-RAY DIFFRACTION99.8895
3.262-3.5230.234440.2809X-RAY DIFFRACTION99.7661
3.523-3.8590.236340.179754X-RAY DIFFRACTION99.2443
3.859-4.3140.248390.172684X-RAY DIFFRACTION99.7241
4.314-4.980.162250.168624X-RAY DIFFRACTION99.3874
4.98-6.0980.322360.218522X-RAY DIFFRACTION99.6429
6.098-8.6150.188220.207431X-RAY DIFFRACTION99.7797
8.615-68.550.253220.181262X-RAY DIFFRACTION100

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