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- PDB-5a5p: Crystal structure of human ATAD2 bromodomain in complex with 8-2-... -

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Basic information

Entry
Database: PDB / ID: 5a5p
TitleCrystal structure of human ATAD2 bromodomain in complex with 8-2-(dimethylamino)ethylamino-3-methyl-1,2-dihydroquinolin-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


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-JTF / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsChung, C. / Bamborough, P. / Demont, E.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Fragment-Based Discovery of Low-Micromolar Atad2 Bromodomain Inhibitors.
Authors: Demont, E.H. / Chung, C. / Furze, R.C. / Grandi, P. / Michon, A. / Wellaway, C. / Barrett, N. / Bridges, A.M. / Craggs, P.D. / Diallo, H. / Dixon, D.P. / Douault, C. / Emmons, A.J. / Jones, ...Authors: Demont, E.H. / Chung, C. / Furze, R.C. / Grandi, P. / Michon, A. / Wellaway, C. / Barrett, N. / Bridges, A.M. / Craggs, P.D. / Diallo, H. / Dixon, D.P. / Douault, C. / Emmons, A.J. / Jones, E.J. / Karamshi, B.V. / Locke, K. / Mitchell, D.J. / Mouzon, B.H. / Prinjha, R.K. / Roberts, A.D. / Sheppard, R.J. / Watson, R.J. / Bamborough, P.
History
DepositionJun 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references

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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)15,9195
Polymers15,4541
Non-polymers4664
Water3,873215
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.393, 79.393, 136.901
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 / 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, EC: 3.6.1.3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-JTF / 8-{[2-(dimethylamino)ethyl]amino}-3-methyl-1,2-dihydroquinolin-2-one


Mass: 245.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N3O
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 4.03 Å3/Da / Density % sol: 69.48 % / Description: NONE
Crystal growDetails: 0.1M TRISHCL PH 7.0-8.0, 1.2-1.5M AMMONIUM SULPHATE,20-25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.03→68.76 Å / Num. obs: 17065 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.1
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.03→68.76 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.663 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20805 862 5.1 %RANDOM
Rwork0.18759 ---
obs0.18864 16163 99.67 %-
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: 28.414 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.26 Å20 Å2
2---0.51 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.03→68.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 31 215 1330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191142
X-RAY DIFFRACTIONr_bond_other_d0.0010.02808
X-RAY DIFFRACTIONr_angle_refined_deg0.8491.9851542
X-RAY DIFFRACTIONr_angle_other_deg0.77831957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0835131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69823.60761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07515213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.4861513
X-RAY DIFFRACTIONr_chiral_restr0.0470.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02233
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: 2.033→2.086 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 58 -
Rwork0.224 1009 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: -12.5944 Å / Origin y: 41.0268 Å / Origin z: 3.4205 Å
111213212223313233
T0.0204 Å2-0.0281 Å20.013 Å2-0.1248 Å2-0.0506 Å2--0.0708 Å2
L2.2291 °20.1466 °2-0.9098 °2-0.0166 °2-0.0811 °2--1.312 °2
S0.0185 Å °-0.3033 Å °0.123 Å °-0.009 Å °-0.0001 Å °-0.0068 Å °-0.0126 Å °0.0454 Å °-0.0185 Å °

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