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- PDB-9mpg: BRD2-BD1 in complex with cyclic peptide 2.1A -

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Basic information

Entry
Database: PDB / ID: 9mpg
TitleBRD2-BD1 in complex with cyclic peptide 2.1A
Components
  • 2.1A
  • Bromodomain-containing protein 2
KeywordsGENE REGULATION / BRD2 / cyclic peptide
Function / homology
Function and homology information


acetylation-dependent protein binding / histone H3K14ac reader activity / chromatin looping / histone H4K5ac reader activity / RUNX3 regulates p14-ARF / histone H4K12ac reader activity / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...acetylation-dependent protein binding / histone H3K14ac reader activity / chromatin looping / histone H4K5ac reader activity / RUNX3 regulates p14-ARF / histone H4K12ac reader activity / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / histone binding / spermatogenesis / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPatel, K. / Mackay, J.P. / Walshe, J.L.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: BRD2-BD1 in complex with cyclic peptide 2.1A
Authors: Patel, K. / Mackay, J.P. / Walshe, J.L.
History
DepositionDec 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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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
D: Bromodomain-containing protein 2
E: 2.1A
F: 2.1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7159
Polymers67,4396
Non-polymers2763
Water7,837435
1
A: Bromodomain-containing protein 2
F: 2.1A
hetero molecules

D: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)33,8114
Polymers33,7193
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area3370 Å2
ΔGint-23 kcal/mol
Surface area14210 Å2
MethodPISA
2
C: Bromodomain-containing protein 2
E: 2.1A
hetero molecules

B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9035
Polymers33,7193
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3180 Å2
ΔGint-23 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 81.543, 69.012
Angle α, β, γ (deg.)90.000, 101.040, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Bromodomain-containing protein 2 / O27.1.1


Mass: 15836.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Protein/peptide 2.1A


Mass: 2046.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953735 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953735 Å / Relative weight: 1
ReflectionResolution: 1.8→48.82 Å / Num. obs: 62636 / % possible obs: 100 % / Redundancy: 5.5 % / Biso Wilson estimate: 24.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.918 / Num. unique obs: 3694 / CC1/2: 0.678 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.82 Å / SU ML: 0.2304 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2178 3161 5.05 %
Rwork0.1821 59430 -
obs0.1839 62591 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 18 435 4721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00894394
X-RAY DIFFRACTIONf_angle_d0.94235929
X-RAY DIFFRACTIONf_chiral_restr0.0545618
X-RAY DIFFRACTIONf_plane_restr0.0074746
X-RAY DIFFRACTIONf_dihedral_angle_d14.99511673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.30331400.2712599X-RAY DIFFRACTION99.89
1.83-1.860.28691510.25142537X-RAY DIFFRACTION99.85
1.86-1.890.28691610.23262558X-RAY DIFFRACTION100
1.89-1.920.28721450.22652551X-RAY DIFFRACTION99.93
1.92-1.950.25971520.21532536X-RAY DIFFRACTION100
1.95-1.990.24851570.19972561X-RAY DIFFRACTION100
1.99-2.030.24721280.1982589X-RAY DIFFRACTION100
2.03-2.080.21731270.18232591X-RAY DIFFRACTION100
2.08-2.120.23251490.17952536X-RAY DIFFRACTION99.93
2.12-2.180.21971500.17382567X-RAY DIFFRACTION99.96
2.18-2.240.26511090.1732620X-RAY DIFFRACTION99.96
2.24-2.30.2471250.17492583X-RAY DIFFRACTION100
2.3-2.380.22761420.16852587X-RAY DIFFRACTION100
2.38-2.460.21681360.16832577X-RAY DIFFRACTION100
2.46-2.560.19911290.17532595X-RAY DIFFRACTION100
2.56-2.680.21481230.17342571X-RAY DIFFRACTION100
2.68-2.820.22231280.17782622X-RAY DIFFRACTION99.93
2.82-2.990.22761550.1832561X-RAY DIFFRACTION100
2.99-3.220.23481240.18832596X-RAY DIFFRACTION99.96
3.22-3.550.20511300.17982607X-RAY DIFFRACTION99.96
3.55-4.060.17421280.1632618X-RAY DIFFRACTION100
4.06-5.120.17551450.16332598X-RAY DIFFRACTION99.93
5.12-48.820.23231270.20222670X-RAY DIFFRACTION99.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.736952347190.008298236922681.152744548293.366478961390.6904494339354.468990663040.08374720670750.300520702523-0.567543900304-0.1245074686120.179125882182-0.3755506789530.4653535307221.10273923976-0.2625851993060.3542857487020.1210462997580.03028065718980.325238037338-0.07015810775120.31797738258720.9883865025-2.39187498552-4.9265076834
21.03691093518-0.8533655457930.9844672722792.51359895917-0.5918239513863.562897626320.07538601082860.0537855743766-0.0101835309482-0.163789905604-0.080770188947-0.1387482913040.008301513360640.2649715614720.02538644800350.1134215011020.004788061587780.008987275108160.1552485681550.006115014660880.20933363182324.25384541641.7772442146513.5231379225
32.312556664880.3726024781890.2282322854464.61473915231-5.941990433497.91090745371-0.05253826504630.2726066545-0.126826135982-0.448632606458-0.0328385766416-0.5246108341780.5275062533080.1958267567280.1717425001710.2134546943120.05559173281880.01529308145140.147440684957-0.05288070664360.20132474743522.8923134517-6.3991410238.95482733991
40.264244963834-0.08015687846450.7320256030423.76403319718-4.198438242436.75564890114-0.00893439792737-0.001738505605690.0255056621267-0.0947655416165-0.03172774767120.01411447444340.1268778434670.0476759761150.0409335640980.1436480576730.03577069946330.01163006548010.16884902703-0.0266394342090.18000522260116.5283046575-2.409411603637.93601766555
59.205565668837.42841243264-4.14960258978.3150001532-2.928762024041.947076653560.299604525671-0.866291309386-0.3356184618011.61505980524-0.3369560333930.1740160564291.118836674660.1175546583740.02412315683890.414527213078-0.01312098493920.04127001911630.2720523460670.0431577904340.22198873801117.3595481448-8.4658551043428.0063185651
67.93089515559-5.105344270663.472690992145.54379262634-4.95489988327.321666592880.0701514862744-0.1205122818150.3179947841410.0597578791638-0.130406491134-0.255056160269-0.487032021353-0.1515924585860.04327014981740.2289631233850.0549739703932-0.0272622056640.163032803019-0.05558241299650.16777825263915.41032976234.8479555619819.0156664626
74.1777749212-3.243390727812.384016893816.873687755323.126032883277.04473795372-0.0542966469644-0.227586945290.32524732869-0.2206844604440.1056026267410.286269486556-1.79798549061-0.875294257493-0.1264369024210.5001479052820.121407669504-0.07011452375090.277463032753-0.01261034326060.29218577977710.594951291811.7862384031-2.84409364902
86.54497479733-1.06531522651-4.782618396777.88468699945-0.02979533661233.579866402130.1377376065640.2735265903790.282360558928-0.466564021295-0.1176281124020.985800994814-1.21815634004-0.655973919509-0.3427571624570.4729980247520.152337895612-0.2161652688620.589227256974-0.1104733620170.559588394878-11.22761996288.9406198963210.5046138386
91.28144097065-0.562096410333-0.5552993629521.911780949851.509086619854.53239998788-0.0108234387060.224533386706-0.0352006223713-0.179266727779-0.167066069860.226991282823-0.223739932961-0.3292549310090.1631689503290.127618447092-0.0245291364108-0.02018390653360.215021702823-0.003722795956820.201988803823-3.21454510237.0465939833824.8624024947
101.48001469517-0.442072145606-1.069418747742.22355701054-0.1172459302630.8562630456320.04307769078140.208267415679-0.157422831625-0.181067764607-0.02592653470210.1743902563590.122510437445-0.139677136671-0.05629158464340.101391463019-0.0255161705291-0.01651621198330.1816449103270.00920581775550.1755889835444.257160436460.57497849702719.0985827657
114.1864971416-1.45133732496-5.441586046717.693767157380.4240596720427.480506558330.198887202187-1.039719304250.2069031817990.871681408433-0.138801216839-0.3652387045260.4025080862830.580524581121-0.05349854834380.436208622848-0.168983766811-0.07417284043080.3948582499110.04442548576870.3243201372150.462785956473-18.629138452.1294099317
129.860838556238.13764899905-6.937779878718.75300904022-6.268658144655.02606265310.22772325853-0.0481491035877-0.08931709466210.528724714578-0.213856444929-0.2019013871470.2835365072710.2755775203220.006796096324680.351115934237-0.0416068160196-0.02756247273150.2171647983570.02479554563630.2754814682175.88035391922-17.6948633206-8.96770490574
132.03154658131-1.497237114780.4572236008319.95951590795-1.843449656715.28729923713-0.02499282433760.267712366906-0.310839684456-0.247431144032-0.0763846633866-0.1977596955630.5531904236-0.04342587353290.06195195530120.212272221541-0.0294260993810.03506264212050.219875241025-0.04624760326740.2762335719688.23396901064-12.9223283542-18.0064007943
143.657070757644.57831100085-0.6385625663026.45141873223-2.272613805274.804293118870.239853119992-0.0944015649532-0.0974342994390.196175522643-0.227279834137-0.1343868789150.1634293935730.1076078928050.02343210459490.1506584184090.001172346230250.002732847295660.12201094062-0.01307528284840.12445831888811.08492467262.26152091776-15.8606688101
154.18644911714-2.07566234541.595226710545.66986667355-5.257216910914.906537889440.173718638333-0.2660712375570.2737126375590.901985969083-0.2170683094620.114007835966-0.652356208785-0.2415289933670.05737553135840.317798611289-0.02381410816140.06427285700240.215602780151-0.02420199151280.2626513752123.044655615144.01995215105-10.4997227392
166.88009037638-4.80844989357-0.1393498515548.80118646971-5.009178561096.660767228350.228407274152-0.856231749765-0.625321246310.500650262333-0.107552769885-0.262019313522-0.03741237143080.372713233747-0.1070011640230.350740843645-0.15481878741-0.04054139772820.3230301457760.04597864009610.3126627914258.09003363084-9.9465562845-2.81794325776
175.41379124644-0.0735225955383-5.658448206336.10751620735-1.184107247278.521770275740.265412034753-0.6286457410790.06894688286030.846978068112-0.198635949294-0.2933838334010.103540386374-0.201292227355-0.0567982402120.559804948487-0.255024687555-0.02164040075660.427751937180.02139385156430.261605580712.86403597171-9.793803645365.45359859929
182.266462850530.700368654773-0.3235635242665.31484467626-5.414244385789.293890237840.173495568651-0.0785506800527-0.09493445970140.1731767290320.03408122802570.400337562140.331938770588-0.610696936084-0.2330174988360.21512945776-0.07608069334190.03565133486830.219695668875-0.04980406627420.251232946782-1.9434994658-5.46177131687-9.72426668101
199.566923873972.306084038145.861061845094.571422752534.593543767556.108915177390.1611250111230.789613117309-0.24401574923-1.37348951442-0.07731762904360.475427291561-0.8193555955120.382009364452-0.02500781982790.3864301227840.0253461532043-0.09029395640690.281523145708-0.03038522115030.269815579587-0.654702165886-1.05818782316-25.8371370508
205.158230394133.86545045447-2.825475457227.41093955439-5.261912434048.157599057170.06386229642090.27912176108-0.229572450891-0.1788444020930.0926238077040.2633744711030.559270049772-0.217047609228-0.1662827329760.184708775684-0.0361154664443-0.02228263562510.187003555886-0.06140766503350.20727596538-1.83848624166-14.0872185405-16.5644748712
219.688803605930.9368888223080.7724673218145.560302111923.774139725742.565356432760.100113798682-0.491427505610.1787480062210.419293834991-0.07976496247280.3431887985861.55510338973-1.2763760689-0.06598885719940.601712952259-0.21119918682-0.0113499750640.4743590150190.04446676837410.333402093563-6.57914514429-20.24047854894.75559699306
224.646008653241.02093360145-0.06000110780064.706568810720.5147696450998.301423869150.3162513484290.4500672058960.179379419002-0.5314326769520.0952855029575-0.698203851387-0.3652575697690.843220705086-0.3633771471280.2233173861140.005373251455130.09489785883240.2989495108560.04937314705470.3379588722920.944176338230.228163994811.9853222807
235.44121222276-2.349121779630.3217758512688.947847301061.922944914515.223497021160.011178307735-0.1383797531070.1189470348280.501225349199-0.0710663216135-0.5082293122620.382591427770.2540822528720.08130374263790.224777406514-0.0948200664021-0.04807539074290.2359146455930.01157592410770.26248050652622.089320101124.863840954532.9201882325
247.906678674843.02731372571-4.21479058827.49566920161-4.337013506963.57087154866-0.13608649176-0.144040372485-0.3019922970320.511454862547-0.203518412508-0.7945518537690.07953519314930.2412332299140.4718229304480.262513006646-0.0476338926388-0.04104645901980.195882493076-0.01586029470470.24047008166422.447624991918.571157016723.5977049249
253.592099875021.13195488439-3.59355861064.05653046442-2.757028688957.537663572780.1926483295190.14002502390.125728964634-0.290529084866-0.042968390505-0.1563735699810.2530112851930.0437625242668-0.1940779313570.156770942821-0.022448261989-0.002252255783210.158690263093-0.004391560624940.20329022518117.035796744920.358379645118.4597307592
261.08669587896-0.921601604540.8270149651420.882057287807-0.01806095297126.130407070540.079497674799-0.1826259677160.07265459585330.0910820922957-0.00747060912090.02844220977710.176488874851-0.553506782914-0.1109732954650.1421489715-0.0758870085328-0.008291046094020.211419591871-0.006784854963780.20796741703810.256482969728.627563226527.2427841469
275.69431814431-4.66412806043-5.97485306923.845704275795.118009939677.971504895930.556844309410.75507579532-0.213610642983-0.933878018532-0.573555650382-0.000582438035863-0.487563838051-0.0922162406916-0.0211697467510.4959320605760.1078122269080.08687370752170.503555941170.1117006471690.3595958324815.463783472728.72234239182.31814348927
286.178891674821.74796723074-0.5570335511858.28457864155-3.416562693556.2260190035-0.0465539484943-0.0989162302041-0.153070067255-0.00255057243229-0.0567834112977-0.04863703526570.28574622828-0.03580923077120.1008354648180.110803083843-0.004726612193740.02539117321740.128887662951-0.01646917301480.1123910996713.37003364821.66002082024-24.7576954086
299.41274875115-1.382924206351.617630775625.98985581587-5.374913302987.44790818748-0.117389047243-0.09197967819410.00135356808093-0.00141862547946-0.0967040258218-0.2786316544140.0007681304979970.2076901409460.2142298608810.1814973096320.0585133987668-0.008623201159370.15759803021-0.006940845709410.16368685696231.60364726-10.123877503126.8109045158
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 64 through 76 )AA64 - 761 - 13
22chain 'A' and (resid 77 through 112 )AA77 - 11214 - 49
33chain 'A' and (resid 113 through 131 )AA113 - 13150 - 68
44chain 'A' and (resid 132 through 155 )AA132 - 15569 - 92
55chain 'A' and (resid 156 through 160 )AA156 - 16093 - 97
66chain 'A' and (resid 161 through 179 )AA161 - 17998 - 116
77chain 'A' and (resid 180 through 188 )AA180 - 188117 - 125
88chain 'B' and (resid 64 through 76 )BB64 - 761 - 10
99chain 'B' and (resid 77 through 160 )BB77 - 16011 - 94
1010chain 'B' and (resid 161 through 188 )BB161 - 18895 - 122
1111chain 'C' and (resid 74 through 84 )CC74 - 841 - 11
1212chain 'C' and (resid 85 through 91 )CC85 - 9112 - 18
1313chain 'C' and (resid 92 through 99 )CC92 - 9919 - 26
1414chain 'C' and (resid 100 through 112 )CC100 - 11227 - 39
1515chain 'C' and (resid 113 through 122 )CC113 - 12240 - 49
1616chain 'C' and (resid 123 through 131 )CC123 - 13150 - 58
1717chain 'C' and (resid 132 through 137 )CC132 - 13759 - 64
1818chain 'C' and (resid 138 through 155 )CC138 - 15565 - 82
1919chain 'C' and (resid 156 through 160 )CC156 - 16083 - 87
2020chain 'C' and (resid 161 through 179 )CC161 - 17988 - 106
2121chain 'C' and (resid 180 through 187 )CC180 - 187107 - 114
2222chain 'D' and (resid 72 through 91 )DD72 - 911 - 20
2323chain 'D' and (resid 92 through 112 )DD92 - 11221 - 41
2424chain 'D' and (resid 113 through 131 )DD113 - 13142 - 60
2525chain 'D' and (resid 132 through 155 )DD132 - 15561 - 84
2626chain 'D' and (resid 156 through 179 )DD156 - 17985 - 108
2727chain 'D' and (resid 180 through 187 )DD180 - 187109 - 116
2828chain 'E' and (resid 1 through 16 )EF1 - 162 - 17
2929chain 'F' and (resid 1 through 16 )FI1 - 162 - 17

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