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- PDB-6ept: The ATAD2 bromodomain in complex with compound 12 -

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Basic information

Entry
Database: PDB / ID: 6ept
TitleThe ATAD2 bromodomain in complex with compound 12
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-BQQ / Chem-G1E / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionOct 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Nov 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 1.3Jan 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)16,2424
Polymers15,4541
Non-polymers7893
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.740, 79.740, 139.211
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-1364-

HOH

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Components

#1: Protein ATPase family AAA domain-containing protein 2 / AAA nuclear coregulator cancer-associated protein / ANCCA


Mass: 15453.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, EC: 3.6.1.3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-G1E / (2~{R})-~{N}-[5-(5-azanylpyridin-3-yl)-4-ethanoyl-1,3-thiazol-2-yl]piperazine-2-carboxamide


Mass: 346.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N6O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BQQ / (2~{S})-~{N}-[5-(5-azanylpyridin-3-yl)-4-ethanoyl-1,3-thiazol-2-yl]piperazine-2-carboxamide


Mass: 346.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N6O2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 4.13 Å3/Da / Density % sol: 70.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2M ammonium sulfate, 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: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→49.023 Å / Num. obs: 59426 / % possible obs: 99.6 % / Redundancy: 6.07 % / CC1/2: 1 / Rrim(I) all: 0.044 / Net I/σ(I): 21.33
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.22 % / Mean I/σ(I) obs: 1.17 / Num. unique obs: 9409 / CC1/2: 0.645 / Rrim(I) all: 0.044 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F36

5f36


Resolution: 1.65→49.023 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.22
RfactorNum. reflection% reflection
Rfree0.2262 2000 6.22 %
Rwork0.2018 --
obs0.2033 32137 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→49.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 53 131 1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071171
X-RAY DIFFRACTIONf_angle_d1.751593
X-RAY DIFFRACTIONf_dihedral_angle_d9.4031015
X-RAY DIFFRACTIONf_chiral_restr0.277174
X-RAY DIFFRACTIONf_plane_restr0.004209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6502-1.69150.30221370.30172059X-RAY DIFFRACTION97
1.6915-1.73720.2971390.26982099X-RAY DIFFRACTION100
1.7372-1.78830.2751410.26042108X-RAY DIFFRACTION100
1.7883-1.84610.25771390.2192113X-RAY DIFFRACTION100
1.8461-1.91210.22771410.21672120X-RAY DIFFRACTION100
1.9121-1.98860.2431410.22262123X-RAY DIFFRACTION100
1.9886-2.07910.2571400.21862120X-RAY DIFFRACTION100
2.0791-2.18870.2261420.20082136X-RAY DIFFRACTION100
2.1887-2.32590.24511430.20712155X-RAY DIFFRACTION100
2.3259-2.50540.19971430.20562145X-RAY DIFFRACTION100
2.5054-2.75760.24221440.21572173X-RAY DIFFRACTION100
2.7576-3.15650.24551450.20652190X-RAY DIFFRACTION100
3.1565-3.97660.23031470.18582217X-RAY DIFFRACTION100
3.9766-49.0450.19081580.18462379X-RAY DIFFRACTION100

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