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- PDB-7qx9: BAZ2A bromodomain in complex with acetylpyrrole derivative compound 65 -

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Basic information

Entry
Database: PDB / ID: 7qx9
TitleBAZ2A bromodomain in complex with acetylpyrrole derivative compound 65
ComponentsBromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


NoRC complex / : / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / : / negative regulation of transcription by RNA polymerase I / : ...NoRC complex / : / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / : / negative regulation of transcription by RNA polymerase I / : / heterochromatin formation / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / nucleolus / regulation of DNA-templated transcription / DNA binding / RNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-G2U / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Caflisch, A. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing.
Authors: Dalle Vedove, A. / Cazzanelli, G. / Batiste, L. / Marchand, J.R. / Spiliotopoulos, D. / Corsi, J. / D'Agostino, V.G. / Caflisch, A. / Lolli, G.
History
DepositionJan 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6962
Polymers12,3641
Non-polymers3321
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.528, 34.961, 37.562
Angle α, β, γ (deg.)90.000, 91.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / Tip5 / hWALp3


Mass: 12363.872 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 1796-1899)
Mutation: First two residues SM derive from the expression tag; double mutant E1845H/L1848S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF9
#2: Chemical ChemComp-G2U / 3-[[4-(4-ethanoyl-3,5-dimethyl-1~{H}-pyrrol-2-yl)-1,3-thiazol-2-yl]methyl]imidazolidine-2,4-dione


Mass: 332.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.25 % / Mosaicity: 0.21 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→37.542 Å / Num. obs: 15741 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.037 / Rrim(I) all: 0.094 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.536.30.71748237600.8220.3070.7812100
8.22-37.545.10.0975881160.9920.0450.10820.299.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MGJ

5mgj


Resolution: 1.5→37.542 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 684 4.35 %
Rwork0.1834 15033 -
obs0.1845 15717 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.76 Å2 / Biso mean: 26.6518 Å2 / Biso min: 10.25 Å2
Refinement stepCycle: final / Resolution: 1.5→37.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 39 115 1007
Biso mean--32.73 31.59 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009939
X-RAY DIFFRACTIONf_angle_d1.0451277
X-RAY DIFFRACTIONf_chiral_restr0.052124
X-RAY DIFFRACTIONf_plane_restr0.006170
X-RAY DIFFRACTIONf_dihedral_angle_d21.28563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.5-1.61580.27191730.24992933
1.6158-1.77840.29881660.24412954
1.7784-2.03570.22971140.19973022
2.0357-2.56470.20591140.17683038
2.5647-37.5420.18511170.16653086
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01560.01130.0012-0.00140.01220.00670.14750.10090.0403-0.191-0.0617-0.0093-0.1136-0.0044-00.1647-0.0119-0.00080.14730.02980.154716.6165-1.88926.1956
20.2451-0.20780.19590.2633-0.0080.355-0.1433-0.28970.3360.0004-0.0482-0.2561-0.2099-0.0133-0.04730.13490.00210.01130.18270.00160.126811.4066-5.204525.9578
30.0169-0.0107-0.01840.02110.0260.034-0.0562-0.1597-0.1221-0.00890.1133-0.08140.0169-0.06320.00780.1542-0.0072-0.00670.14190.04690.160610.5293-16.727923.8494
40.0483-0.0527-0.09290.15490.22420.33880.11350.106-0.08360.0106-0.2228-0.1190.1265-0.0075-0.02660.16010.03620.01850.14310.03410.154319.6011-9.495711.6808
50.0293-0.06220.00290.136-0.02540.0130.05350.0204-0.0835-0.1328-0.05480.0801-0.0635-0.1684-0.00180.1256-0.0011-0.00160.11680.00750.13977.2095-11.727514.4831
60.0596-0.04670.03020.1750.04550.07320.01450.0710.0204-0.1112-0.01090.1527-0.1548-0.1781-0.00360.14690.0459-0.01130.1750.02210.13432.3895-3.019513.4718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1796 through 1810 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1811 through 1829 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1830 through 1839 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1840 through 1854 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1855 through 1872 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1873 through 1898 )A0

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