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- PDB-7r0y: ATAD2 in complex with PepLite-Glu -

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Basic information

Entry
Database: PDB / ID: 7r0y
TitleATAD2 in complex with PepLite-Glu
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 extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity ...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 extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / 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-HNU / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 2, 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)16,0327
Polymers15,4541
Non-polymers5796
Water4,143230
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)79.288, 79.288, 138.015
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-1330-

HOH

21AAA-1465-

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, 236 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-HNU / (2~{S})-2-acetamido-~{N}-prop-2-enyl-pentanediamide


Mass: 227.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O3 / 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.: 230 / 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: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.43→61.48 Å / Num. obs: 47816 / % possible obs: 99.5 % / Redundancy: 19.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.027 / Rrim(I) all: 0.091 / Net I/σ(I): 17.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.83-61.4815.40.0543640.9980.0180.057
1.43-1.4510.32.94322010.1951.3533.252

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Processing

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

3dai


Resolution: 1.43→61.48 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.058 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2135 2335 4.891 %
Rwork0.1951 45409 -
all0.196 --
obs-47744 99.34 %
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: 34.361 Å2
Baniso -1Baniso -2Baniso -3
1-0.162 Å20.081 Å20 Å2
2--0.162 Å2-0 Å2
3----0.526 Å2
Refinement stepCycle: LAST / Resolution: 1.43→61.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 35 230 1349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0121180
X-RAY DIFFRACTIONr_angle_refined_deg2.6331.6581596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5475139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34220.6182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23215218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1371514
X-RAY DIFFRACTIONr_chiral_restr0.1510.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02929
X-RAY DIFFRACTIONr_nbd_refined0.2330.2598
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3190.2172
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.6390.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4980.241
X-RAY DIFFRACTIONr_mcbond_it3.0242.641544
X-RAY DIFFRACTIONr_mcangle_it4.3853.944687
X-RAY DIFFRACTIONr_scbond_it6.1923.354636
X-RAY DIFFRACTIONr_scangle_it9.0674.798909
X-RAY DIFFRACTIONr_lrange_it12.97340.771954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.4670.3321600.3183169X-RAY DIFFRACTION95.3322
1.467-1.5070.2941550.2763140X-RAY DIFFRACTION97.6586
1.507-1.5510.2681490.2683131X-RAY DIFFRACTION98.9741
1.551-1.5990.2551510.2533061X-RAY DIFFRACTION99.9378
1.599-1.6510.2671560.2252976X-RAY DIFFRACTION99.9681
1.651-1.7090.251640.2162852X-RAY DIFFRACTION100
1.709-1.7740.2661470.2232775X-RAY DIFFRACTION100
1.774-1.8460.2321250.2112700X-RAY DIFFRACTION100
1.846-1.9280.2511280.2162584X-RAY DIFFRACTION99.9631
1.928-2.0220.2251190.2062482X-RAY DIFFRACTION100
2.022-2.1320.2271360.2032332X-RAY DIFFRACTION100
2.132-2.2610.2181160.1932246X-RAY DIFFRACTION100
2.261-2.4170.21150.1942096X-RAY DIFFRACTION100
2.417-2.610.1931000.1831972X-RAY DIFFRACTION100
2.61-2.860.2151020.1781829X-RAY DIFFRACTION100
2.86-3.1970.189720.1771681X-RAY DIFFRACTION100
3.197-3.6910.191940.1631469X-RAY DIFFRACTION100
3.691-4.520.165710.1451277X-RAY DIFFRACTION100
4.52-6.3890.216440.2061032X-RAY DIFFRACTION100
6.389-61.480.246310.271605X-RAY DIFFRACTION96.3636

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