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- PDB-6hic: The ATAD2 bromodomain in complex with compound 15 -

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Basic information

Entry
Database: PDB / ID: 6hic
TitleThe ATAD2 bromodomain in complex with compound 15
ComponentsATPase family AAA domain-containing protein 2
KeywordsCYTOSOLIC PROTEIN / Bromodomain / ATAD2 / inhibitor / complex
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. / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 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. / Bromodomain-like / Histone Acetyltransferase; Chain A / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chem-G7H / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.768 Å
AuthorsSledz, P. / Caflisch, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers.
Authors: Dolbois, A. / Batiste, L. / Wiedmer, L. / Dong, J. / Brutsch, M. / Huang, D. / Deerain, N.M. / Spiliotopoulos, D. / Cheng-Sanchez, I. / Laul, E. / Nevado, C. / Sledz, P. / Caflisch, A.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,3774
Polymers15,4541
Non-polymers9233
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.852, 79.852, 138.123
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1365-

HOH

21A-1467-

HOH

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Components

#1: Protein ATPase family AAA domain-containing protein 2 / Bromodomain of ATAD2


Mass: 15453.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18
#2: Chemical ChemComp-G7H / (2~{R})-~{N}-[4-ethanoyl-5-[4-(2-oxidanylidenepyrrolidin-1-yl)phenyl]-1,3-thiazol-2-yl]piperazine-2-carboxamide


Mass: 413.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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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: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 1.768→39.926 Å / Num. obs: 48152 / % possible obs: 99.6 % / Redundancy: 6.03 % / CC1/2: 0.999 / Rrim(I) all: 0.0071 / Net I/σ(I): 16.02
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 2.84 % / Num. unique obs: 7608 / CC1/2: 0.533 / Rrim(I) all: 1.39 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5f36

5f36


Resolution: 1.768→39.926 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 23.69
RfactorNum. reflection% reflection
Rfree0.2248 2409 5.02 %
Rwork0.2019 --
obs0.203 47996 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.768→39.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 58 168 1289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081145
X-RAY DIFFRACTIONf_angle_d1.3031556
X-RAY DIFFRACTIONf_dihedral_angle_d9.7961011
X-RAY DIFFRACTIONf_chiral_restr0.047169
X-RAY DIFFRACTIONf_plane_restr0.005204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7675-1.80360.46871340.45792499X-RAY DIFFRACTION93
1.8036-1.84280.48161500.41892679X-RAY DIFFRACTION100
1.8428-1.88570.41761360.38222689X-RAY DIFFRACTION100
1.8857-1.93280.29511390.3562699X-RAY DIFFRACTION100
1.9328-1.98510.34511410.32132675X-RAY DIFFRACTION100
1.9851-2.04350.28831370.27372697X-RAY DIFFRACTION100
2.0435-2.10950.24561440.23052688X-RAY DIFFRACTION100
2.1095-2.18490.27091440.21112686X-RAY DIFFRACTION100
2.1849-2.27230.22261440.21132721X-RAY DIFFRACTION100
2.2723-2.37570.21861410.19562700X-RAY DIFFRACTION100
2.3757-2.5010.18191470.18122673X-RAY DIFFRACTION100
2.501-2.65760.19441390.19432716X-RAY DIFFRACTION100
2.6576-2.86280.27711440.1992675X-RAY DIFFRACTION100
2.8628-3.15080.22961380.20022702X-RAY DIFFRACTION100
3.1508-3.60640.20111400.18542694X-RAY DIFFRACTION100
3.6064-4.54270.17661430.16152691X-RAY DIFFRACTION100
4.5427-39.93620.20651480.18092703X-RAY DIFFRACTION100

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