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- PDB-6hi4: The ATAD2 bromodomain in complex with compound 7 -

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Basic information

Entry
Database: PDB / ID: 6hi4
TitleThe ATAD2 bromodomain in complex with compound 7
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. / ATPase family associated with various cellular activities (AAA) / Bromodomain-like / Histone Acetyltransferase; Chain A / 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. / ATPase family associated with various cellular activities (AAA) / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / 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-G5W / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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)15,8693
Polymers15,4541
Non-polymers4152
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area7880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.669, 79.669, 137.884
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-1311-

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-G5W / (2~{R})-2-azanyl-~{N}-[4-ethanoyl-5-(3-methoxyphenyl)-1,3-thiazol-2-yl]propanamide


Mass: 319.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O3S
#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.: 176 / 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

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: 1.00036 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00036 Å / Relative weight: 1
ReflectionResolution: 1.69→48.768 Å / Num. obs: 54799 / % possible obs: 99.8 % / Redundancy: 6.88 % / CC1/2: 0.999 / Rrim(I) all: 0.058 / Net I/σ(I): 18.27
Reflection shellResolution: 1.69→1.79 Å / Redundancy: 6.58 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 8790 / CC1/2: 0.595 / Rrim(I) all: 1.177 / % possible all: 99.2

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Processing

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

5f36


Resolution: 1.69→48.768 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2208 2718 4.97 %
Rwork0.2015 --
obs0.2025 54725 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.69→48.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 20 176 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081119
X-RAY DIFFRACTIONf_angle_d1.0331520
X-RAY DIFFRACTIONf_dihedral_angle_d6.264974
X-RAY DIFFRACTIONf_chiral_restr0.086171
X-RAY DIFFRACTIONf_plane_restr0.005201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6904-1.72110.39551360.34242657X-RAY DIFFRACTION97
1.7211-1.75420.32031400.31152762X-RAY DIFFRACTION100
1.7542-1.790.29881450.29572743X-RAY DIFFRACTION100
1.79-1.82890.31251470.29062744X-RAY DIFFRACTION100
1.8289-1.87150.25331390.27932730X-RAY DIFFRACTION100
1.8715-1.91830.31831430.26932740X-RAY DIFFRACTION100
1.9183-1.97010.27551470.25242749X-RAY DIFFRACTION100
1.9701-2.02810.25731450.23992731X-RAY DIFFRACTION100
2.0281-2.09360.24861390.23942756X-RAY DIFFRACTION100
2.0936-2.16840.23741410.22332735X-RAY DIFFRACTION100
2.1684-2.25520.25481480.22392727X-RAY DIFFRACTION100
2.2552-2.35790.25941420.21152752X-RAY DIFFRACTION100
2.3579-2.48220.18631440.21062735X-RAY DIFFRACTION100
2.4822-2.63770.22761440.21282754X-RAY DIFFRACTION100
2.6377-2.84130.21981370.20862739X-RAY DIFFRACTION100
2.8413-3.12720.2331420.20152748X-RAY DIFFRACTION100
3.1272-3.57960.19671460.17742732X-RAY DIFFRACTION100
3.5796-4.50940.18571490.16432727X-RAY DIFFRACTION100
4.5094-48.78850.19311440.17462746X-RAY DIFFRACTION100

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