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- PDB-4a9f: N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-METHYLPYRROLIDIN-2-ONE -

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Basic information

Entry
Database: PDB / ID: 4a9f
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-METHYLPYRROLIDIN-2-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
1-methylpyrrolidin-2-one / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 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, A.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 8, 2012Group: Other
Revision 1.2May 8, 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)54,37410
Polymers53,7263
Non-polymers6487
Water8,089449
1
A: BROMODOMAIN-CONTAINING PROTEIN 2
B: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2707
Polymers35,8172
Non-polymers4525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-19.1 kcal/mol
Surface area11360 Å2
MethodPISA
2
C: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules

C: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2086
Polymers35,8172
Non-polymers3904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2340 Å2
ΔGint-37.9 kcal/mol
Surface area11550 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-MB3 / 1-methylpyrrolidin-2-one


Mass: 99.131 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 38.92 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7
Details: 0.1M HEPES PH 7, 24-28% PEG 3350, 0.2 M (NH4)2SO4, 20 DEGREES CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.73→23.6 Å / Num. obs: 42840 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.3 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→23.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.067 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21389 2160 5 %RANDOM
Rwork0.17696 ---
obs0.17886 40680 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.083 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å2-1.14 Å2
2---0.44 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.73→23.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 40 449 3196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222910
X-RAY DIFFRACTIONr_bond_other_d0.0010.021959
X-RAY DIFFRACTIONr_angle_refined_deg0.9311.943952
X-RAY DIFFRACTIONr_angle_other_deg0.78534800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2055339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69424.891137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44615526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.901159
X-RAY DIFFRACTIONr_chiral_restr0.0510.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02571
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_it0.6521687
X-RAY DIFFRACTIONr_mcbond_other0.0962653
X-RAY DIFFRACTIONr_mcangle_it1.24142755
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.59741223
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.49861197
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: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 138 -
Rwork0.319 2806 -
obs--100 %
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)
11.619-0.6173-0.05281.2244-0.04291.2777-0.0682-0.0217-0.10770.0880.02060.181-0.0344-0.09570.04760.04940.01230.02030.0507-0.00560.079716.43817.10550.9279
20.9555-0.264-0.19252.38180.20681.61350.0223-0.0605-0.00170.25360.0315-0.1512-0.00310.0397-0.05380.090.0016-0.04920.02040.00520.067634.79628.542910.6696
30.8485-0.09550.92241.8668-0.26523.2162-0.09010.09770.0161-0.18290.1557-0.0276-0.18970.1461-0.06550.0383-0.00830.00720.17250.01080.0052-1.744318.788623.3215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 182
2X-RAY DIFFRACTION2B76 - 185
3X-RAY DIFFRACTION3C76 - 182

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