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- PDB-9nn3: BET BRD2-BD1 in complex with peptide 6.2 -

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Basic information

Entry
Database: PDB / ID: 9nn3
TitleBET BRD2-BD1 in complex with peptide 6.2
Components
  • Bromodomain-containing protein 2
  • peptide 6.2
KeywordsTRANSCRIPTION / inhibitor / complex
Function / homology
Function and homology information


histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / histone H4K5ac reader activity / histone H4K12ac reader activity / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / histone H4K5ac reader activity / 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: 1.6 Å
AuthorsJing, X. / Deshpande, C. / Patel, K. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Chem.Commun.(Camb.) / Year: 2026
Title: The effect of peptide size on target affinity in mRNA display-derived macrocyclic peptides.
Authors: Jing, X. / Suh, J. / Maxwell, J. / Patel, K. / Norman, A. / Reid, X.J. / Deshpande, C. / Low, J.K.K. / Payne, R.J. / Passioura, T. / Mackay, J.P.
History
DepositionMar 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 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: peptide 6.2
D: peptide 6.2


Theoretical massNumber of molelcules
Total (without water)28,9284
Polymers28,9284
Non-polymers00
Water6,485360
1
A: Bromodomain-containing protein 2
D: peptide 6.2


Theoretical massNumber of molelcules
Total (without water)14,4642
Polymers14,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-10 kcal/mol
Surface area7320 Å2
MethodPISA
2
B: Bromodomain-containing protein 2
C: peptide 6.2


Theoretical massNumber of molelcules
Total (without water)14,4642
Polymers14,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-9 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.728, 66.932, 90.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 13262.429 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25440
#2: Protein/peptide peptide 6.2


Mass: 1201.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M tri-Sodium citrate pH 5.5 PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→45.14 Å / Num. obs: 42021 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 15.18 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 32.3
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.122 / Num. unique obs: 42020

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALAdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.08 Å / SU ML: 0.1289 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.0957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1818 2131 5.07 %
Rwork0.1565 39888 -
obs0.1577 42019 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 8 360 2374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992076
X-RAY DIFFRACTIONf_angle_d1.10572812
X-RAY DIFFRACTIONf_chiral_restr0.0513288
X-RAY DIFFRACTIONf_plane_restr0.0078356
X-RAY DIFFRACTIONf_dihedral_angle_d6.5811268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.20831300.16292612X-RAY DIFFRACTION99.82
1.64-1.680.1851400.15532633X-RAY DIFFRACTION100
1.68-1.720.17351600.1522601X-RAY DIFFRACTION100
1.72-1.770.19681580.15632599X-RAY DIFFRACTION100
1.77-1.830.19221400.16012619X-RAY DIFFRACTION100
1.83-1.90.18061400.15782639X-RAY DIFFRACTION100
1.9-1.970.1891370.16012632X-RAY DIFFRACTION99.96
1.97-2.060.17181400.15482653X-RAY DIFFRACTION100
2.06-2.170.18841480.14922641X-RAY DIFFRACTION100
2.17-2.310.17061330.14992651X-RAY DIFFRACTION100
2.31-2.490.18921360.14942676X-RAY DIFFRACTION100
2.49-2.740.16371410.16012683X-RAY DIFFRACTION100
2.74-3.130.1981350.15892674X-RAY DIFFRACTION100
3.13-3.940.17861450.14672719X-RAY DIFFRACTION100
3.95-45.080.17811480.1692856X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 25.995 Å / Origin y: 10.02 Å / Origin z: -9.786 Å
111213212223313233
T0.0657084504827 Å20.0142156847348 Å2-0.0114585401964 Å2-0.0696566217081 Å20.00045772174526 Å2--0.0838879899951 Å2
L0.278541235093 °20.0580077818889 °2-0.198362520256 °2-0.304674106771 °2-0.0771383866708 °2--0.719597703969 °2
S-0.0104052357469 Å °-0.000580243553539 Å °-0.0084679161 Å °-0.0155358763099 Å °0.0380849285124 Å °0.0210558000718 Å °0.0129497794122 Å °-0.0364796049058 Å °0.0338373084998 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )A76 - 186
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )A201 - 371
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )B75 - 183
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )B201 - 361
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )C1 - 10
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )C11
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )C101 - 119
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )D1 - 10
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )D11
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 76:186 OR RESID 201:371 ) ) OR ( CHAIN B AND ( RESID 75:183 OR RESID 201:361 ) ) OR ( CHAIN C AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:119 ) ) OR ( CHAIN D AND ( RESID 1:10 OR RESID 11:11 OR RESID 101:109 ) )D101 - 109

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