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- PDB-8dnq: BRD2-BD1 in complex with cyclic peptide 2.2B -

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Basic information

Entry
Database: PDB / ID: 8dnq
TitleBRD2-BD1 in complex with cyclic peptide 2.2B
Components
  • Bromodomain-containing protein 2
  • Cyclic peptide 2.2B
KeywordsTRANSCRIPTION / cyclic peptide / bromodomain / brd2 / BET
Function / homology
Function and homology information


chromosome / chromatin organization / nuclear speck / nucleoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / : / 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: 1.84 Å
AuthorsPatel, K. / Franck, C. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Structure / Year: 2023
Title: Discovery and characterization of cyclic peptides selective for the C-terminal bromodomains of BET family proteins.
Authors: Franck, C. / Patel, K. / Walport, L.J. / Christie, M. / Norman, A. / Passioura, T. / Suga, H. / Payne, R.J. / Mackay, J.P.
History
DepositionJul 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Cyclic peptide 2.2B
D: Cyclic peptide 2.2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2289
Polymers35,7684
Non-polymers4605
Water3,531196
1
A: Bromodomain-containing protein 2
C: Cyclic peptide 2.2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1605
Polymers17,8842
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-17 kcal/mol
Surface area7540 Å2
MethodPISA
2
B: Bromodomain-containing protein 2
D: Cyclic peptide 2.2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0684
Polymers17,8842
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-17 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.682, 54.370, 76.924
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2


Mass: 15765.340 Da / Num. of mol.: 2 / Fragment: BD1 (UNP residues 65-194)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2 / Production host: Escherichia coli (E. coli) / References: UniProt: U3KQA6
#2: Protein/peptide Cyclic peptide 2.2B


Mass: 2118.457 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2018
RadiationMonochromator: 0.9537 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→44.37 Å / Num. obs: 29565 / % possible obs: 98.2 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.089 / Rrim(I) all: 0.13 / Χ2: 0.53 / Net I/σ(I): 6.9
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1801 / CC1/2: 0.733 / Rpim(I) all: 0.647 / Rrim(I) all: 0.762 / Χ2: 0.48 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ONI

3oni


Resolution: 1.84→44.37 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 1527 5.18 %
Rwork0.2088 --
obs0.2115 29500 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 30 196 2468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072361
X-RAY DIFFRACTIONf_angle_d0.8273195
X-RAY DIFFRACTIONf_dihedral_angle_d19.337323
X-RAY DIFFRACTIONf_chiral_restr0.045323
X-RAY DIFFRACTIONf_plane_restr0.005397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.90.35091440.30652505X-RAY DIFFRACTION98
1.9-1.960.34461450.2812452X-RAY DIFFRACTION96
1.96-2.040.32421390.23242560X-RAY DIFFRACTION100
2.04-2.140.31721550.23722468X-RAY DIFFRACTION96
2.14-2.250.26491420.21022494X-RAY DIFFRACTION97
2.25-2.390.27931180.21242559X-RAY DIFFRACTION98
2.39-2.570.24861280.20112609X-RAY DIFFRACTION100
2.57-2.830.24141350.20482557X-RAY DIFFRACTION98
2.83-3.240.2231350.19632613X-RAY DIFFRACTION100
3.24-4.090.23221550.17912490X-RAY DIFFRACTION96
4.09-44.370.24731310.1952666X-RAY DIFFRACTION99
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)
12.88050.1484-1.28732.03310.36543.56050.0281-0.17270.27530.35260.0058-0.1063-0.1038-0.14320.02460.21440.0204-0.03610.1409-0.01250.1189-6.0203-13.7735-1.7212
25.48052.61582.2643.53763.62043.9749-0.02360.0459-0.0211-0.11190.0292-0.7423-0.30960.6392-0.01010.1711-0.01840.01750.2142-0.05120.26644.467-19.5192-15.0961
32.2111-1.08480.48810.6877-0.77181.9798-0.06280.15310.2328-0.1682-0.0084-0.19130.1686-0.00080.05790.2459-0.03550.00950.11640.00920.1957-6.7422-14.9564-25.9792
40.78910.44460.53271.92941.45734.5207-0.1113-0.05140.0644-0.1466-0.05110.1038-0.507-0.39060.18670.14630.0576-0.03080.130.01350.1477-12.6165-14.0829-16.852
50.5832-0.0366-0.10372.03341.30973.27950.0792-0.0279-0.0024-0.0224-0.11130.0568-0.0259-0.44540.02650.118-0.0041-0.00830.13480.00820.1393-12.0529-20.1729-13.2846
60.7762-0.1859-0.8760.85210.38339.0148-0.1886-0.1192-0.03130.2096-0.0065-0.1110.27020.47330.20690.14060.018-0.01460.0998-0.0020.1065-1.9937-25.8903-11.7414
76.4416-4.7296-1.10643.62421.57583.5729-0.2357-0.4686-0.01680.40820.22890.04170.3498-0.1952-0.08790.316-0.03590.01410.27880.01060.1676-11.2349-17.84947.2479
80.6072-0.6684-0.10731.35310.00434.5720.03740.0175-0.0089-0.03690.0271-0.06360.25630.1359-0.08850.17280.00310.0030.1158-0.00310.1581-2.75364.1231-30.366
97.1562-1.16845.59045.4757-3.7797.293-0.1659-0.58440.1730.77940.1146-0.07530.041-0.76460.02940.41070.02790.06590.20450.01680.1358-12.35015.4439-7.9817
100.3756-0.02610.07921.47380.87482.36290.0180.0239-0.0236-0.0089-0.07330.07750.1399-0.26440.05490.1291-0.0220.0040.14590.00320.1457-11.88766.0811-26.8056
112.28792.30562.3449.25661.43932.59670.079-0.2080.17850.28070.04380.27070.0142-0.17760.0260.31360.0610.04860.069-0.05160.0792-7.269319.1383-12.6248
120.43670.0856-0.28590.90010.9533.0882-0.16590.00750.0179-0.2641-0.0932-0.0455-0.70420.56570.13660.1639-0.01850.02960.0967-0.00010.1114-0.884515.4231-26.9531
134.85211.27591.31950.8973-0.73172.81790.10170.531-0.0218-0.33760.1372-0.02920.02560.2634-0.20150.2633-0.00550.03790.22860.00060.1554-7.23827.3007-46.9817
145.68010.87320.30063.90370.11864.1873-0.0087-0.12530.31560.31450.03-0.0337-0.47460.217-0.00340.2246-0.00330.01540.1504-0.01390.11181.6295-19.0223-28.1843
155.4918-0.8536-0.05892.7020.17044.3553-0.0191-0.0771-0.23190.0456-0.0573-0.0480.61470.36880.09060.301-0.00420.00220.16640.02690.12670.48488.6009-10.1984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 160 )
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 179 )
7X-RAY DIFFRACTION7chain 'A' and (resid 180 through 187 )
8X-RAY DIFFRACTION8chain 'B' and (resid 71 through 104 )
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 112 )
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 155 )
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 160 )
12X-RAY DIFFRACTION12chain 'B' and (resid 161 through 179 )
13X-RAY DIFFRACTION13chain 'B' and (resid 180 through 187 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 15 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 15 )

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