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- PDB-4a9h: N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-(2-methyl-1,2,3,4-tet... -

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Basic information

Entry
Database: PDB / ID: 4a9h
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-(2-methyl-1,2,3,4-tetrahydroquinolin-1-yl)ethan-1-one
ComponentsBROMODOMAIN-CONTAINING PROTEIN 2
KeywordsSIGNALING PROTEIN / INHIBITOR / HISTONE / EPIGENETIC READER
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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-TVP / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChung, C.W. / Bamborough, P.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Fragment-Based Discovery of Bromodomain Inhibitors Part 1: Inhibitor Binding Modes and Implications for Lead Discovery.
Authors: Chung, C.W. / Dean, T.W. / Woolven, J.M. / Bamborough, P.
History
DepositionNov 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BROMODOMAIN-CONTAINING PROTEIN 2
B: BROMODOMAIN-CONTAINING PROTEIN 2
C: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,61010
Polymers53,7263
Non-polymers8847
Water5,765320
1
A: BROMODOMAIN-CONTAINING PROTEIN 2
B: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4167
Polymers35,8172
Non-polymers5995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-20.5 kcal/mol
Surface area11850 Å2
MethodPISA
2
C: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules

C: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3886
Polymers35,8172
Non-polymers5714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2520 Å2
ΔGint-39 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.232, 55.531, 67.975
Angle α, β, γ (deg.)90.00, 94.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BROMODOMAIN-CONTAINING PROTEIN 2 / HUMAN BRD2


Mass: 17908.727 Da / Num. of mol.: 3 / Fragment: N-TERMINAL BROMODOMAIN (BD1), RESIDUES 67-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TVP / (2S)-1-ACETYL-2-METHYL-1,2,3,4-TETRAHYDROQUINOLINE


Mass: 189.254 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H15NO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.82 % / Description: NONE
Crystal growTemperature: 293 K / pH: 8
Details: 0.1M HEPES, PH 8.0 30% PEG3350, 0.2M (NH4)2SO4, 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.05→67.88 Å / Num. obs: 26554 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 2
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→67.88 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.925 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20463 1342 5.1 %RANDOM
Rwork0.15862 ---
obs0.16106 25212 99.88 %-
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: 32.883 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å2-2.19 Å2
2---1.91 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.05→67.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 60 320 3108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022980
X-RAY DIFFRACTIONr_bond_other_d0.0010.022030
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.944051
X-RAY DIFFRACTIONr_angle_other_deg0.83534979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3985349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71425.036139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82615546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.816159
X-RAY DIFFRACTIONr_chiral_restr0.0620.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02596
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 78 -
Rwork0.255 1804 -
obs--99.95 %
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)
10.7984-0.2342-0.32450.6835-0.04681.0853-0.08330.0139-0.0380.08150.03320.06180.0118-0.03370.050.03320.01150.02720.033-0.00160.058715.89386.66252.0158
20.9389-0.1654-0.21630.64610.03021.1820.007-0.0388-0.02680.10180.0539-0.0791-0.04840.0145-0.06090.0520.0136-0.01010.02320.00230.057334.49948.617610.455
30.4557-0.04260.672.10280.12731.7308-0.06480.0108-0.0002-0.1340.1170.0278-0.07160.1032-0.05220.02150.0062-0.00170.10280.01320.0079-1.689718.934323.648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 186
2X-RAY DIFFRACTION2B76 - 182
3X-RAY DIFFRACTION3C76 - 182

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