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- PDB-7vri: crystal structure of BRD2-BD2 in complex with guanosine analog -

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Basic information

Entry
Database: PDB / ID: 7vri
Titlecrystal structure of BRD2-BD2 in complex with guanosine analog
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION/INHIBITOR / BET family / BET inhibitor / Bromodomain Inhibitor / BRD2-BD1 inhibitor / TRANSCRIPTION-INHIBITOR COMPLEX
Function / homology
Function and homology information


acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
9-HYROXYETHOXYMETHYLGUANINE / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPadmanabhan, B. / Arole, A. / Deshmukh, P. / Ashok, S. / Mathur, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural and biochemical insights into purine-based drug molecules in hBRD2 delineate a unique binding mode opening new vistas in the design of inhibitors of the BET family.
Authors: Arole, A.H. / Deshmukh, P. / Sridhar, A. / Mathur, S. / Mahalingaswamy, M. / Subramanya, H. / Dalavaikodihalli Nanjaiah, N. / Padmanabhan, B.
History
DepositionOct 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,4401
Non-polymers2251
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint3 kcal/mol
Surface area6860 Å2
Unit cell
Length a, b, c (Å)52.316, 71.476, 32.028
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-751-

HOH

21A-813-

HOH

31A-816-

HOH

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Components

#1: Protein Bromodomain-containing protein 2


Mass: 13440.270 Da / Num. of mol.: 1 / Mutation: K358S, K363S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25440
#2: Chemical ChemComp-AC2 / 9-HYROXYETHOXYMETHYLGUANINE


Mass: 225.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N5O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antivirus*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: PEG MME 2000, 50mM Tris, 50mM Nacl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.45→13.79 Å / Num. obs: 21402 / % possible obs: 96.3 % / Redundancy: 4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.127 / Net I/σ(I): 14.15
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.566 / Num. unique obs: 857 / CC1/2: 0.89 / % possible all: 77.3

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Processing

Software
NameVersionClassification
PHENIX(1.18_3855: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XHK

5xhk


Resolution: 1.5→13.79 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 971 4.99 %
Rwork0.1832 --
obs0.1854 19444 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→13.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 16 219 1165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051018
X-RAY DIFFRACTIONf_angle_d0.7881382
X-RAY DIFFRACTIONf_dihedral_angle_d5.401162
X-RAY DIFFRACTIONf_chiral_restr0.045134
X-RAY DIFFRACTIONf_plane_restr0.005202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.33151270.25292427X-RAY DIFFRACTION92
1.58-1.680.24311350.20432575X-RAY DIFFRACTION97
1.68-1.810.24651400.19572652X-RAY DIFFRACTION99
1.81-1.990.26791400.18612662X-RAY DIFFRACTION100
1.99-2.270.22581380.17322641X-RAY DIFFRACTION98
2.28-2.860.22141430.18212690X-RAY DIFFRACTION99
2.86-13.790.19671480.17062826X-RAY DIFFRACTION99

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