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- PDB-6hdn: Crystal structure of human ATAD2 bromodomain in complex with 3-me... -

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Basic information

Entry
Database: PDB / ID: 6hdn
TitleCrystal structure of human ATAD2 bromodomain in complex with 3-methyl-8-((8-methyl-8-azabicyclooctan-3-yl)amino)-1,7-naphthyridin-2(1H)-one
ComponentsATPase family AAA domain-containing protein 2
KeywordsTRANSCRIPTION / INHIBITOR / ATAD2 / BROMODOMAIN / EPIGENETICS / ATPase family AAA domain-containing protein 2
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-like / Histone Acetyltransferase; Chain A / 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) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / 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-FZB / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsChung, C.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Aiming to Miss a Moving Target: Bromo and Extra Terminal Domain (BET) Selectivity in Constrained ATAD2 Inhibitors.
Authors: Bamborough, P. / Chung, C.W. / Furze, R.C. / Grandi, P. / Michon, A.M. / Watson, R.J. / Mitchell, D.J. / Barnett, H. / Prinjha, R.K. / Rau, C. / Sheppard, R.J. / Werner, T. / Demont, E.H.
History
DepositionAug 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)16,1647
Polymers15,4541
Non-polymers7116
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Ligand binding characterised FRET and SPR
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-19 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.070, 79.070, 138.388
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-1203-

SO4

21A-1203-

SO4

31A-1413-

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
Details: SM remains from tag cleavage / Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, EC: 3.6.1.3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FZB / 3-methyl-8-((8-methyl-8-azabicyclooctan-3-yl)amino)-1,7-naphthyridin-2(1H)-one


Mass: 298.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N4O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 4.04 Å3/Da / Density % sol: 69.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 1.2-1.5M ammonium sulphate and 20-25% PEG3350. / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→68.48 Å / Num. obs: 20781 / % possible obs: 99.6 % / Redundancy: 11.28 % / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.97 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementResolution: 1.9→68.48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.15 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22956 1066 5.1 %RANDOM
Rwork0.19378 ---
obs0.19561 19709 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----1.61 Å2
Refinement stepCycle: 1 / Resolution: 1.9→68.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 45 198 1327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191169
X-RAY DIFFRACTIONr_bond_other_d0.0010.021121
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.9891585
X-RAY DIFFRACTIONr_angle_other_deg0.73632584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1365135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32223.49263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07715216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1361514
X-RAY DIFFRACTIONr_chiral_restr0.0580.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2625.926526
X-RAY DIFFRACTIONr_mcbond_other2.2615.908524
X-RAY DIFFRACTIONr_mcangle_it3.27413.266656
X-RAY DIFFRACTIONr_mcangle_other3.27213.278657
X-RAY DIFFRACTIONr_scbond_it5.3496.716641
X-RAY DIFFRACTIONr_scbond_other5.3446.721642
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.59214.793923
X-RAY DIFFRACTIONr_long_range_B_refined9.74228.981557
X-RAY DIFFRACTIONr_long_range_B_other9.74628.9681556
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 80 -
Rwork0.237 1414 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -12.4122 Å / Origin y: 41.0101 Å / Origin z: 3.327 Å
111213212223313233
T0.0079 Å2-0.0189 Å20.0151 Å2-0.1019 Å2-0.0192 Å2--0.0864 Å2
L1.495 °20.3105 °2-0.2849 °2-0.0815 °20.0919 °2--1.5133 °2
S0.005 Å °-0.2284 Å °0.0394 Å °-0.0039 Å °-0.0452 Å °0.0024 Å °-0.0087 Å °-0.0358 Å °0.0402 Å °

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