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- PDB-5a81: Crystal structure of human ATAD2 bromodomain in complex with 8-(3... -

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Basic information

Entry
Database: PDB / ID: 5a81
TitleCrystal structure of human ATAD2 bromodomain in complex with 8-(3R,4R) -3-(cyclohexylmethoxy)piperidin-4-yl-amino-3-methyl-1,2-dihydro-1,7- naphthyridin-2-one
ComponentsATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
KeywordsHYDROLASE / INHIBITOR / ATAD2 / BROMODOMAIN / EPIGENETICS / ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
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-78J / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsChung, C. / Bamborough, P. / Demont, E.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structure-Based Optimization of Naphthyridones Into Potent Atad2 Bromodomain Inhibitors.
Authors: Bamborough, P. / Chung, C. / Furze, R.C. / Grandi, P. / Michon, A. / Sheppard, R.J. / Barnett, H. / Diallo, H. / Dixon, D.P. / Douault, C. / Jones, E.J. / Karamshi, B. / Mitchell, D.J. / ...Authors: Bamborough, P. / Chung, C. / Furze, R.C. / Grandi, P. / Michon, A. / Sheppard, R.J. / Barnett, H. / Diallo, H. / Dixon, D.P. / Douault, C. / Jones, E.J. / Karamshi, B. / Mitchell, D.J. / Prinjha, R.K. / Rau, C. / Watson, R.J. / Werner, T. / Demont, E.H.
History
DepositionJul 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)16,1406
Polymers15,4541
Non-polymers6875
Water3,675204
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.540, 79.540, 138.220
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-3055-

HOH

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Components

#1: Protein ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2 / AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN / ANCCA / HUMAN ATPASE FAMILY AAA DOMAIN- ...AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN / ANCCA / HUMAN ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2


Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: BROMODOMAIN, RESIDUES 981-1108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6PL18, adenosinetriphosphatase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-78J / (3R,4R)-3-(cyclohexylmethoxy)piperidin-4-yl]amino}-3-methyl-1,2-dihydro-1,7-naphthyridin-2-one


Mass: 370.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N4O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSM INITIAL TWO RESIDUES LEFT OVER FROM TAG CLEAVAGE

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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: 4.08 Å3/Da / Density % sol: 69.88 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Type: DIAMOND / Wavelength: 0.9763
DetectorDate: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.03→61.65 Å / Num. obs: 17310 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→48.79 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.399 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21938 877 5.1 %RANDOM
Rwork0.19659 ---
obs0.19771 16394 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.306 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.03→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 45 204 1330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191164
X-RAY DIFFRACTIONr_bond_other_d0.0010.02834
X-RAY DIFFRACTIONr_angle_refined_deg0.911.9921574
X-RAY DIFFRACTIONr_angle_other_deg0.80732020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1195133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1523.49263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69515213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7921514
X-RAY DIFFRACTIONr_chiral_restr0.0540.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02237
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 65 -
Rwork0.256 1023 -
obs--99.82 %
Refinement TLS params.Method: refined / Origin x: -12.5551 Å / Origin y: 41.0423 Å / Origin z: 3.5258 Å
111213212223313233
T0.0203 Å2-0.025 Å20.0129 Å2-0.1057 Å2-0.0317 Å2--0.0537 Å2
L1.9108 °20.2467 °2-0.6586 °2-0.0695 °20.0669 °2--0.9628 °2
S0.0027 Å °-0.2411 Å °0.0503 Å °-0.0171 Å °-0.014 Å °0.0021 Å °-0.029 Å °0.0555 Å °0.0113 Å °

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