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- PDB-6eps: The ATAD2 bromodomain in complex with compound UZH-DQ41 -

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Basic information

Entry
Database: PDB / ID: 6eps
TitleThe ATAD2 bromodomain in complex with compound UZH-DQ41
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-BQK / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.081 Å
AuthorsSledz, P. / Caflisch, A.
CitationJournal: To Be Published
Title: Hitting a moving target: simulation and crystallography study of ATAD2 bromodomain blockers
Authors: Sledz, P.
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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)15,9123
Polymers15,4541
Non-polymers4582
Water1,45981
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 area7920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.801, 79.801, 138.879
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 / 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, adenosinetriphosphatase
#2: Chemical ChemComp-BQK / (2~{R})-~{N}-[5-[3,5-bis(oxidanyl)phenyl]-4-ethanoyl-1,3-thiazol-2-yl]piperazine-2-carboxamide


Mass: 362.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O4S
#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.: 81 / 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: 70.22 %
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: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.08→48.984 Å / Num. obs: 29118 / % possible obs: 97.8 % / Redundancy: 6.82 % / CC1/2: 0.998 / Rrim(I) all: 0.132 / Net I/σ(I): 12.79
Reflection shellResolution: 2.08→2.21 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 4558 / CC1/2: 0.717 / Rrim(I) all: 1 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
PHASERphasing
RefinementResolution: 2.081→48.984 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.15
RfactorNum. reflection% reflection
Rfree0.2743 1452 4.99 %
Rwork0.2276 --
obs0.2298 29095 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.081→48.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 30 81 1178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081121
X-RAY DIFFRACTIONf_angle_d1.1131521
X-RAY DIFFRACTIONf_dihedral_angle_d6.825976
X-RAY DIFFRACTIONf_chiral_restr0.046170
X-RAY DIFFRACTIONf_plane_restr0.005199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0807-2.1550.28911340.27772633X-RAY DIFFRACTION92
2.155-2.24130.32091390.28312763X-RAY DIFFRACTION99
2.2413-2.34330.3311480.3042815X-RAY DIFFRACTION99
2.3433-2.46690.31081500.32292765X-RAY DIFFRACTION99
2.4669-2.62140.42311410.3192691X-RAY DIFFRACTION95
2.6214-2.82380.3911480.31642806X-RAY DIFFRACTION99
2.8238-3.10790.27361500.26472807X-RAY DIFFRACTION99
3.1079-3.55750.24871490.20652818X-RAY DIFFRACTION100
3.5575-4.48160.23621480.16792753X-RAY DIFFRACTION98
4.4816-48.99770.21671450.16912792X-RAY DIFFRACTION99

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