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- PDB-6c3n: Crystal structure of BCL6 BTB domain in complex with compound 7CC5 -

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Basic information

Entry
Database: PDB / ID: 6c3n
TitleCrystal structure of BCL6 BTB domain in complex with compound 7CC5
ComponentsB-cell lymphoma 6 protein
KeywordsTRANSCRIPTION/Inhibitor / Inhibitor / protein-protein interaction / TRANSCRIPTION-Inhibitor complex
Function / homology
Function and homology information


negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / regulation of germinal center formation / paraspeckles / negative regulation of B cell apoptotic process / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / FOXO-mediated transcription of cell death genes / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain ...negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / regulation of germinal center formation / paraspeckles / negative regulation of B cell apoptotic process / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / FOXO-mediated transcription of cell death genes / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of cell differentiation / regulation of immune response / regulation of cytokine production / transcription corepressor binding / chromatin DNA binding / negative regulation of cell growth / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of apoptotic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / DNA damage response / negative regulation of transcription by RNA polymerase II / DNA-templated transcription / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(2-phenylethyl)-N'-pyridin-3-ylthiourea / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53170577659 Å
AuthorsLinhares, B. / Cheng, H. / Xue, F. / Cierpicki, T.
CitationJournal: J.Med.Chem. / Year: 2018
Title: Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.
Authors: Cheng, H. / Linhares, B.M. / Yu, W. / Cardenas, M.G. / Ai, Y. / Jiang, W. / Winkler, A. / Cohen, S. / Melnick, A. / MacKerell Jr., A. / Cierpicki, T. / Xue, F.
History
DepositionJan 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3474
Polymers29,8332
Non-polymers5152
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Protein-observed NMR spectroscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-29 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.103, 85.065, 117.750
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 B-cell lymphoma 6 protein / BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing ...BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing protein 27 / Zinc finger protein 51


Mass: 14916.308 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P41182
#2: Chemical ChemComp-EHY / N-(2-phenylethyl)-N'-pyridin-3-ylthiourea


Mass: 257.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.6 M ammonium formate, .1 M Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 11920 / % possible obs: 84.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 38.6909775015 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.116 / Net I/σ(I): 16.6
Reflection shellResolution: 2.53→2.62 Å / Rmerge(I) obs: 0.438 / Num. unique obs: 1054 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R29

1r29


Resolution: 2.53170577659→35.6391223756 Å / SU ML: 0.395730089065 / Cross valid method: FREE R-VALUE / σ(F): 1.37523975902 / Phase error: 27.5104225428
RfactorNum. reflection% reflection
Rfree0.267523859751 514 5.05855722862 %
Rwork0.207037382309 --
obs0.210066088749 10161 84.3936877076 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.3315426658 Å2
Refinement stepCycle: LAST / Resolution: 2.53170577659→35.6391223756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 36 86 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003664949775162003
X-RAY DIFFRACTIONf_angle_d0.6746286285182703
X-RAY DIFFRACTIONf_chiral_restr0.0435972252272323
X-RAY DIFFRACTIONf_plane_restr0.00329538539133341
X-RAY DIFFRACTIONf_dihedral_angle_d13.00845650371219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5317-2.78640.3683627604441290.2804406981592497X-RAY DIFFRACTION89.3805309735
2.7864-3.18940.3608140127151320.2490523832382415X-RAY DIFFRACTION86.3682604273
3.1894-4.01740.2477582957661260.2019646640692291X-RAY DIFFRACTION80.5935311771
4.0174-35.64260.2148522245061270.1714673110092444X-RAY DIFFRACTION81.619047619
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)
16.85148911067-5.4288509611-1.369158168068.595662976552.903499766578.90266502469-0.694501851033-0.938306724531-0.01835557744960.2725961674810.663433729747-0.8858668943730.8899565240031.33162561580.1269929971170.4698996868570.07404632790760.03359501595050.5979772897580.1318765205860.42191791992614.9374402527-48.943336335816.2729314417
25.605487076262.258132938580.115720523766.37456562894-0.8581903248335.20090433919-0.164530912255-0.267160233693-0.2259741625250.07977798861840.30061045486-0.1416225225740.676522997850.2520328913980.02311455772220.3467868444850.02086773690340.01308687659990.3762256081680.009358097601560.2457434696148.41697612747-31.616149985721.5600954949
35.62375172971-3.87693389138-4.575622072834.271836119383.52394146616.504595661310.0604582230666-0.4867612537740.441160393685-0.6328492069870.249262524307-0.20026337091-0.9934884028870.423282379419-0.2813640781370.386193349575-0.0734261507913-0.08782444175540.33244282141-0.006642954592410.4841421727724.39202031494-10.536481035619.8438209969
45.10908318574-4.893644597263.232623083588.55818325403-1.333448662546.352395920350.180188772554-0.5132457140430.117923592945-0.174893170992-0.06740665367650.4247145796120.303361773952-0.176127462669-0.08326241661820.300353984663-0.02138142256410.01628511330660.428593997569-0.01325045293890.323600119196-5.97343914226-18.885389599319.3505985547
55.445388602965.323773952665.178508503215.197364698495.06398675044.92656981519-0.0248840480021-0.421173614759-0.51603431057-0.310782659955-0.277645145476-0.2321935461170.6602018515710.55600894450.2188738238250.6281990083620.06826956224020.01537820084070.4496621037260.05003728226750.451605705754-8.55451618925-14.26143844510.4384124421
61.40704525712.643814430830.7011529308859.65499869168-3.213744930225.964034887970.16443469784-0.1719098371340.2420984910720.5626318269330.0661224611908-0.0779030788585-0.3280916693070.0761785322003-0.1933109670560.3545034214830.04199465459140.06911190607710.374800250891-0.05601520654690.363848718432-0.884375667084-11.36537043828.0764505585
76.42329539844-3.7533634825-2.540501550233.756838841762.468409623395.32814143321-0.55091237235-0.4935689170910.8441434439750.727371642891.04517643089-0.3432994581890.6748408539761.46182703057-0.2163505155280.65854810860.133696899808-0.01403622158350.351635515233-0.0160742054630.3648642854863.71057474139-19.595472705136.1943458671
85.399139386692.969743512191.026194669828.161529692625.651279933756.359574488810.00480690067856-0.443639634912-0.2459374890780.754642076688-0.292447792721-0.1638211290580.268332017228-1.058743055530.2070272400460.4136145557860.09321748564050.04795920543990.3361503482540.003118182470030.357107986856-7.19616782412-14.658504999833.592789754
93.4131474781-2.72901231453-4.321357584197.667518814182.730954546815.92604710562-1.06217345302-0.0408184062209-0.5421040193241.14111156595-0.2179649737290.9557846538861.17431612472-0.7394236735270.9658682308540.769640189663-0.07977533527070.1295724190680.415072679852-0.05088024319560.500482719817-7.29517194522-21.679309604641.7028414416
104.11013307946-1.25742616841.195219537285.408264380810.001199847976489.03990933139-0.190512127523-0.245130637004-0.7740175245330.646096178030.2316946720250.296321627225-0.259058695607-0.378886345167-0.01202546076260.466990878902-0.02226164631020.06665345370990.283021693976-0.009131737216620.402778227641-2.14437454903-29.402002898523.5235048064
114.39032014326-1.90394509014-0.2499690661475.031708813060.3325345684426.5438337620.01998014031610.6909545758460.1940456324850.33754299605-0.3158094199440.1484098617110.08662588073730.05587706982840.2326237084570.259451463012-0.0349075116710.05320050938070.3406108199240.0001448730774760.2870537067632.97728076339-29.15718454155.9473841506
125.489423012020.604155712693-1.681682258455.70874634541-4.399337514867.8726612820.1352578790250.2458442494870.5130118959460.747797180869-0.0667233587778-0.083255434736-0.7307654586250.0789134560741-0.0471735854140.444432927123-0.0172326546930.04378045065080.426779393416-0.03474317966960.36667637964913.4877076558-23.67566567195.56360311278
137.82913634159-2.877430412411.695576958042.368758936071.581066392794.077198866540.1513655404270.631010439131-0.525933520638-1.56486981089-0.28645993997-0.5296750897781.01772379160.397026875801-0.1145830180710.5287519489980.0819888980340.0977242371530.497395316734-0.0354439930670.36650899880510.1670918613-36.3111340928-1.96797519776
144.31122253113-2.39357045875-4.630452380168.83816231133-3.077386927869.22258618321-0.2829946849630.620626183793-0.697250657471-0.952149923342-0.380903889973-0.0736886044470.866614100046-0.5850329535510.6957133266910.5560163397920.004844744205230.09248160344170.3010541282480.0009395512938840.3923325588433.80070284576-39.88854679858.46382181455
150.9634403788721.533989369681.959286716626.179196895-0.2094509731596.751718578410.239258178009-0.254424465390.172716282096-0.5847062614660.1256523234030.2840779209590.26346565519-0.528881637309-0.2241649090570.301762147023-0.03858529549340.005829153800040.380545604478-0.01641622588480.4406258947852.65929794004-45.25450391613.5020348473
166.62772085094-0.190388059566-1.252176360695.45219777539-4.817237274936.74543936291-0.29760287878-0.0650863187094-0.282811917023-0.7218866034020.0326805808157-0.817265368611.459085738040.8740347023690.264565742680.5385896494910.1044484120580.07913243841650.4542595446070.02304972697390.33263368032313.2914074524-42.72940949137.90830637364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 115 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 61 )
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 70 )
6X-RAY DIFFRACTION6chain 'A' and (resid 71 through 90 )
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 101 )
8X-RAY DIFFRACTION8chain 'A' and (resid 102 through 114 )
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 129 )
10X-RAY DIFFRACTION10chain 'B' and (resid 7 through 28 )
11X-RAY DIFFRACTION11chain 'B' and (resid 29 through 54 )
12X-RAY DIFFRACTION12chain 'B' and (resid 55 through 70 )
13X-RAY DIFFRACTION13chain 'B' and (resid 71 through 79 )
14X-RAY DIFFRACTION14chain 'B' and (resid 80 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 101 )
16X-RAY DIFFRACTION16chain 'B' and (resid 102 through 114 )

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