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- PDB-7qxt: ATAD2 in complex with FragLite10 -

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Basic information

Entry
Database: PDB / ID: 7qxt
TitleATAD2 in complex with FragLite10
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 / 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
6-bromo-1,3-dihydro-2H-indol-2-one / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 27, 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 1.2Jan 11, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 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)16,0177
Polymers15,4541
Non-polymers5646
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.191, 81.191, 134.966
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-1354-

HOH

21AAA-1376-

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, EC: 3.6.1.3

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Non-polymers , 5 types, 159 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-1P8 / 6-bromo-1,3-dihydro-2H-indol-2-one


Mass: 212.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6BrNO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.51→70.31 Å / Num. obs: 41986 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.054 / Rrim(I) all: 0.183 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.27-70.31170.0783370.9970.0240.082
1.51-1.549.69.56920110.2394.46610.598

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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: 1.51→70.31 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.311 / SU ML: 0.099 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2558 2104 5.024 %
Rwork0.2218 39773 -
all0.224 --
obs-41877 99.826 %
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: 45.639 Å2
Baniso -1Baniso -2Baniso -3
1-1.817 Å20.908 Å20 Å2
2--1.817 Å2-0 Å2
3----5.894 Å2
Refinement stepCycle: LAST / Resolution: 1.51→70.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 30 153 1267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131180
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171103
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.6611598
X-RAY DIFFRACTIONr_angle_other_deg1.4761.5892553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1065138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01820.87580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51915220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8751515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021328
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02261
X-RAY DIFFRACTIONr_nbd_refined0.2120.2267
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.2935
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2563
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2542
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2760.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.210
X-RAY DIFFRACTIONr_nbd_other0.2320.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1180.21
X-RAY DIFFRACTIONr_mcbond_it4.2214.307543
X-RAY DIFFRACTIONr_mcbond_other4.2194.297542
X-RAY DIFFRACTIONr_mcangle_it5.2226.412684
X-RAY DIFFRACTIONr_mcangle_other5.2196.424685
X-RAY DIFFRACTIONr_scbond_it6.0485.084636
X-RAY DIFFRACTIONr_scbond_other6.0025.061633
X-RAY DIFFRACTIONr_scangle_it9.0987.383914
X-RAY DIFFRACTIONr_scangle_other9.047.346909
X-RAY DIFFRACTIONr_lrange_it11.10953.331401
X-RAY DIFFRACTIONr_lrange_other11.10653.381402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.5490.61760.5982786X-RAY DIFFRACTION98.047
1.549-1.5920.5241280.5432854X-RAY DIFFRACTION99.9665
1.592-1.6380.5131370.4842750X-RAY DIFFRACTION100
1.638-1.6880.4061570.4222633X-RAY DIFFRACTION100
1.688-1.7440.3811420.3882581X-RAY DIFFRACTION100
1.744-1.8050.3381400.3632520X-RAY DIFFRACTION100
1.805-1.8730.3661220.3192409X-RAY DIFFRACTION100
1.873-1.9490.2931360.3112334X-RAY DIFFRACTION100
1.949-2.0360.2621160.272240X-RAY DIFFRACTION100
2.036-2.1350.2381040.2112170X-RAY DIFFRACTION100
2.135-2.2510.241060.1892058X-RAY DIFFRACTION100
2.251-2.3870.2371000.2111954X-RAY DIFFRACTION100
2.387-2.5520.251950.181838X-RAY DIFFRACTION100
2.552-2.7560.243960.2051719X-RAY DIFFRACTION100
2.756-3.0190.272830.1981595X-RAY DIFFRACTION100
3.019-3.3760.197650.1791472X-RAY DIFFRACTION100
3.376-3.8970.196700.1651297X-RAY DIFFRACTION100
3.897-4.7720.192590.1531121X-RAY DIFFRACTION100
4.772-6.7450.203410.158902X-RAY DIFFRACTION100
6.745-70.310.228310.206540X-RAY DIFFRACTION99.3044

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