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- PDB-6hib: The ATAD2 bromodomain in complex with compound 14 -

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Basic information

Entry
Database: PDB / ID: 6hib
TitleThe ATAD2 bromodomain in complex with compound 14
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-G6Z / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.029 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)15,8813
Polymers15,4541
Non-polymers4272
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-5 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.020, 80.020, 138.337
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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-G6Z / 1-azanyl-~{N}-[5-(5-azanylpyridin-3-yl)-4-ethanoyl-1,3-thiazol-2-yl]cyclobutane-1-carboxamide


Mass: 331.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N5O2S
#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.: 71 / 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: 4.14 Å3/Da / Density % sol: 70.27 %
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: X06DA / Wavelength: 1.000031 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.029→48.956 Å / Num. obs: 32104 / % possible obs: 99.8 % / Redundancy: 5.67 % / CC1/2: 0.999 / Rrim(I) all: 0.107 / Net I/σ(I): 13.42
Reflection shellResolution: 2.03→2.15 Å / Redundancy: 5.04 % / Num. unique obs: 5177 / CC1/2: 0.523 / Rrim(I) all: 1.36 / % possible all: 99.2

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Processing

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

5f36


Resolution: 2.029→48.956 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.24
RfactorNum. reflection% reflection
Rfree0.2306 1763 10.01 %
Rwork0.2084 --
obs0.2107 17621 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.029→48.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 28 71 1169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081134
X-RAY DIFFRACTIONf_angle_d1.1391542
X-RAY DIFFRACTIONf_dihedral_angle_d9.494993
X-RAY DIFFRACTIONf_chiral_restr0.045172
X-RAY DIFFRACTIONf_plane_restr0.007202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0292-2.0840.32221300.29211172X-RAY DIFFRACTION99
2.084-2.14540.29741330.27011189X-RAY DIFFRACTION100
2.1454-2.21460.28871320.25931198X-RAY DIFFRACTION100
2.2146-2.29380.3361330.29181192X-RAY DIFFRACTION100
2.2938-2.38560.25591330.22571202X-RAY DIFFRACTION100
2.3856-2.49420.22941340.21381194X-RAY DIFFRACTION100
2.4942-2.62570.2591330.21271194X-RAY DIFFRACTION100
2.6257-2.79010.27461330.22151212X-RAY DIFFRACTION100
2.7901-3.00550.25211360.231221X-RAY DIFFRACTION100
3.0055-3.30790.2431360.21131223X-RAY DIFFRACTION100
3.3079-3.78650.21481370.18671235X-RAY DIFFRACTION100
3.7865-4.76990.19551410.16691267X-RAY DIFFRACTION100
4.7699-48.96990.19121520.20231359X-RAY DIFFRACTION100

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