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- PDB-9d5o: Crystal structure of the second bromodomain of human BRD2 in comp... -

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Basic information

Entry
Database: PDB / ID: 9d5o
TitleCrystal structure of the second bromodomain of human BRD2 in complex with 3IND
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / BRD2 / BROMODOMAIN / BROMODOMAIN INHIBITOR / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNithianantham, S. / Fischer, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142772 United States
CitationJournal: Bioorg.Chem. / Year: 2025
Title: Positional isomers of Indolyl-benzodiazepines display dissimilar binding and recruitment of BET transcriptional regulators to targeted genomic loci.
Authors: Chowdhury, N. / Nithianantham, S. / Dey, S. / Mohammed, R. / Mohammed, A. / Churion, K. / Lang, W. / Young, S. / Philips, S.J. / Das, S. / Ray, B. / Shelat, A. / Fischer, M. / Ansari, A.Z. / Jaisankar, P.
History
DepositionAug 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8809
Polymers54,0984
Non-polymers1,7825
Water00
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9402
Polymers13,5241
Non-polymers4151
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0603
Polymers13,5241
Non-polymers5362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9402
Polymers13,5241
Non-polymers4151
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9402
Polymers13,5241
Non-polymers4151
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.183, 99.871, 120.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13524.474 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25440
#2: Chemical
ChemComp-A1A12 / methyl [(4S,6M,10aM)-6-(1H-indol-3-yl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]acetate


Mass: 415.445 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H21N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
Has ligand of interestY
Has protein modificationN

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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: 3.45 Å3/Da / Density % sol: 64.33 % / Description: Rectangular
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Ammonium tartrate dibasic pH 7.0, and 18% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 11524 / % possible obs: 89.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 76.11 Å2 / CC1/2: 0.977 / CC star: 0.994 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.105 / Rrim(I) all: 0.186 / Χ2: 0.873 / Net I/av σ(I): 6.456 / Net I/σ(I): 5.9
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.171 / Num. unique obs: 567 / CC1/2: 0.576 / CC star: 0.855 / Rpim(I) all: 0.446 / Rrim(I) all: 0.812 / Χ2: 0.84 / % possible all: 88.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.33 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 502 4.94 %
Rwork0.225 --
obs0.2267 10171 78.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 132 0 3538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023657
X-RAY DIFFRACTIONf_angle_d0.6874981
X-RAY DIFFRACTIONf_dihedral_angle_d14.8451265
X-RAY DIFFRACTIONf_chiral_restr0.036504
X-RAY DIFFRACTIONf_plane_restr0.003637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.520.3378940.28411814X-RAY DIFFRACTION60
3.52-4.030.27841400.24342539X-RAY DIFFRACTION85
4.03-5.080.23671310.21912663X-RAY DIFFRACTION87
5.08-48.330.24751370.20382653X-RAY DIFFRACTION83

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