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- PDB-7bc2: BAZ2A bromodomain in complex with triazole compound MS04-TN04 -

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Basic information

Entry
Database: PDB / ID: 7bc2
TitleBAZ2A bromodomain in complex with triazole compound MS04-TN04
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-T8Z / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Sedykh, M. / Caflisch, A. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
Citation
Journal: 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.
#1: Journal: ACS Bio Med Chem Au / Year: 2021
Title: Identification of a BAZ2A Bromodomain Hit Compound by Fragment Joining
Authors: Dalle Vedove, A. / Cazzanelli, G. / Corsi, J. / Sedykh, M. / D'Agostino, V.G. / Caflisch, A. / Lolli, G.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
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
A: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7232
Polymers12,3641
Non-polymers3591
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.603, 94.603, 32.744
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2051-

HOH

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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: E1845H L1848S
Source method: isolated from a genetically manipulated source
Details: First two residues SM derive from the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF9
#2: Chemical ChemComp-T8Z / 2-(1-methyl-1H-1,2,3-triazol-5-yl)-5-((2-(pyridin-4-yl)pyrrolidin-1-yl)methyl)-1H-benzo[d]imidazole / 2-(3-methyl-1,2,3-triazol-4-yl)-6-[[(2~{S})-2-pyridin-4-ylpyrrolidin-1-yl]methyl]-1~{H}-benzimidazole


Mass: 359.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.42 Å3/Da / Density % sol: 64.05 % / 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: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 2→81.93 Å / Num. obs: 11620 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.022 / Rrim(I) all: 0.097 / Net I/σ(I): 22.8 / Num. measured all: 218667 / Scaling rejects: 1
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
2-2.0515.71.469137798750.7950.381.5182100
8.95-81.9315.20.027233115310.0070.02881.199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5mgj


Resolution: 2→47.302 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 616 5.31 %
Rwork0.1669 10988 -
obs0.1679 11604 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.69 Å2 / Biso mean: 46.4882 Å2 / Biso min: 24.59 Å2
Refinement stepCycle: final / Resolution: 2→47.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 27 77 956
Biso mean--44.98 46.82 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006906
X-RAY DIFFRACTIONf_angle_d0.8461223
X-RAY DIFFRACTIONf_chiral_restr0.042119
X-RAY DIFFRACTIONf_plane_restr0.004159
X-RAY DIFFRACTIONf_dihedral_angle_d18.634527
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.0002-2.20150.24781510.20732711
2.2015-2.52010.21031480.17622740
2.5201-3.17490.20271470.18822726
3.1749-47.3020.16461700.15052811
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)
19.2436-1.6544-0.53632.0880.55679.772-0.2399-0.1464-1.04930.7441-0.2587-0.12150.96790.29970.32610.4791-0.10650.01560.39670.05310.4757-32.414120.04737.4013
20.3972-0.4431.12860.6524-0.38596.4265-0.03950.00190.09450.0871-0.12110.2191-0.0256-0.2150.01310.234-0.06940.0020.4656-0.01140.3432-38.314736.7004-3.5498
31.92580.9545-0.85945.8059-2.66413.3888-0.19220.1634-0.3137-0.44870.0305-0.42620.4742-0.01660.15910.2646-0.0790.05030.3277-0.05460.3116-29.566628.2342-4.4771
43.3839-0.65950.69562.2736-1.35155.98060.0109-0.3563-0.2421-0.01790.008-0.14040.4417-0.24620.06290.2459-0.0917-0.03330.3841-0.00240.3246-27.97234.87937.155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1796 through 1810 )A1796 - 1810
2X-RAY DIFFRACTION2chain 'A' and (resid 1811 through 1829 )A1811 - 1829
3X-RAY DIFFRACTION3chain 'A' and (resid 1830 through 1872 )A1830 - 1872
4X-RAY DIFFRACTION4chain 'A' and (resid 1873 through 1898 )A1873 - 1898

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