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- PDB-7z9s: ATAD2 in complex with PepLite-Arg -

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Basic information

Entry
Database: PDB / ID: 7z9s
TitleATAD2 in complex with PepLite-Arg
ComponentsATPase family AAA domain-containing protein 2
KeywordsTRANSCRIPTION / ATAD2 / INHIBITOR / FRAGMENT / BROMODOMAIN / FRAGLITE
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / 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) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain ...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) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-IJI / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTurberville, S. / Martin, M.P. / Hope, I. / Noble, M.E.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKC57659/A27310 United Kingdom
Cancer Research UKC1362/A20263 United Kingdom
Cancer Research UKC2215/A21421 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions.
Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / ...Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / Endicott, J.A. / Hardcastle, I.R. / Noble, M.E.M. / Waring, M.J.
History
DepositionMar 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,30711
Polymers15,4541
Non-polymers85310
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.370, 79.370, 137.288
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11AAA-1344-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

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


Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6PL18, EC: 3.6.1.3

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Non-polymers , 5 types, 207 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IJI / (2~{S})-2-acetamido-5-carbamimidamido-~{N}-prop-2-enyl-pentanamide


Mass: 253.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate / PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91162 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91162 Å / Relative weight: 1
ReflectionResolution: 1.5→48.57 Å / Num. obs: 41696 / % possible obs: 100 % / Redundancy: 39.6 % / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.025 / Rrim(I) all: 0.118 / Net I/σ(I): 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.22-48.5729.50.02834010.0060.028
1.5-1.5340.29.07520330.4582.0059.295

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAI

3dai


Resolution: 1.5→48.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.504 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2362 2028 4.873 %
Rwork0.2039 39589 -
all0.206 --
obs-41617 99.957 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.291 Å2-0.146 Å2-0 Å2
2---0.291 Å2-0 Å2
3---0.945 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 53 197 1334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121189
X-RAY DIFFRACTIONr_angle_refined_deg2.1311.6681597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7385137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18620.11984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45215218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0721515
X-RAY DIFFRACTIONr_chiral_restr0.1380.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02923
X-RAY DIFFRACTIONr_nbd_refined0.2320.2625
X-RAY DIFFRACTIONr_nbtor_refined0.320.2800
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2141
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4240.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.30.224
X-RAY DIFFRACTIONr_mcbond_it3.0692.96539
X-RAY DIFFRACTIONr_mcangle_it4.2864.405679
X-RAY DIFFRACTIONr_scbond_it6.5693.676650
X-RAY DIFFRACTIONr_scangle_it8.9535.265918
X-RAY DIFFRACTIONr_lrange_it12.22244.1721944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.3241380.3492872X-RAY DIFFRACTION99.9336
1.539-1.5810.3211370.3482799X-RAY DIFFRACTION100
1.581-1.6270.3111400.3282720X-RAY DIFFRACTION100
1.627-1.6770.3181320.282652X-RAY DIFFRACTION100
1.677-1.7320.2681480.2572563X-RAY DIFFRACTION100
1.732-1.7930.2341290.2542479X-RAY DIFFRACTION99.9617
1.793-1.860.2751190.2292410X-RAY DIFFRACTION99.9605
1.86-1.9360.2761050.2262354X-RAY DIFFRACTION100
1.936-2.0230.2241210.2132227X-RAY DIFFRACTION99.9574
2.023-2.1210.2441040.2092125X-RAY DIFFRACTION100
2.121-2.2360.2061110.1982043X-RAY DIFFRACTION100
2.236-2.3720.257980.2021943X-RAY DIFFRACTION100
2.372-2.5350.2461030.2051810X-RAY DIFFRACTION100
2.535-2.7380.231670.2041745X-RAY DIFFRACTION100
2.738-2.9990.232830.1971579X-RAY DIFFRACTION100
2.999-3.3530.262740.2031450X-RAY DIFFRACTION100
3.353-3.8720.209690.1641294X-RAY DIFFRACTION100
3.872-4.7410.143630.1361104X-RAY DIFFRACTION100
4.741-6.7010.257540.21883X-RAY DIFFRACTION100
6.701-48.570.289330.243537X-RAY DIFFRACTION99.6503

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