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6i41

Co-crystal structure of human SPOP MATH domain (wild-type) and human BRD3 fragment

Method: X-RAY DIFFRACTION Dmax: 57.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Speckle-type POZ protein

Homo sapiens

UniProt O43791

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 28–166 Not recorded Bromodomain-containing protein 3 × 1 （Q15059） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；100 mM Tris pH 8.5, 200 mM NaCl, 25% (w/v) PEG3350 Resolution 1.90 Å R-free 0.238

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6I41 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CR2 Solution structure of N-terminal domain of speckle-type POZ protein Deposited 2005-05-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–173（146 aa） Fragment：math domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.25mM math domain U-13C,15N; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3 | 90% H2O/10% D2O
Resolution not provided
3HQI Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1 Deposited 2009-06-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 28–329（302 aa） Fragment：UNP residues 28-329
Chain B 28–329（302 aa） Fragment：UNP residues 28-329
Mutation：D140G Mutation：D140G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；pH 5.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.62 Å R-free 0.275
3HQL Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2 Deposited 2009-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：UNP residues 28-166
Mutation：D140G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 1.66 Å R-free 0.258
3HQL Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2 Deposited 2009-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–166（139 aa） Fragment：UNP residues 28-166
Mutation：D140G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 1.66 Å R-free 0.258
3HQM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2 Deposited 2009-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：UNP residues 28-166
Mutation：D140G SO4 SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.74 Å R-free 0.218
3HQM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2 Deposited 2009-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–166（139 aa） Fragment：UNP residues 28-166
Mutation：D140G SO4 SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.74 Å R-free 0.218
3HSV Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-MacroH2ASBCpep2 Deposited 2009-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 28–166（139 aa）
Chain B 28–166（139 aa）
Mutation：D140G Mutation：D140G ZN ZINC ION × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.43 Å R-free 0.206
3HTM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPBTB/3-box Deposited 2009-06-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 172–329（158 aa） Fragment：UNP residues 172-329
Chain B 172–329（158 aa） Fragment：UNP residues 172-329
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.50 Å R-free 0.256
3HTM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPBTB/3-box Deposited 2009-06-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 172–329（158 aa） Fragment：UNP residues 172-329
Chain D 172–329（158 aa） Fragment：UNP residues 172-329
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.50 Å R-free 0.256
3HU6 Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1 Deposited 2009-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 28–329（302 aa） Fragment：UNP residues 28-329
Chain B 28–329（302 aa） Fragment：UNP residues 28-329
Mutation：D140G Mutation：D140G No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.296
3IVB Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1 Deposited 2009-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：UNP residues 28-166
Not recorded ZN ZINC ION × 5 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；10-20% PEG3350, 0.1 M Tris pH 7.6, 50 mM zinc acetate. Cryoprotection 30% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.75 Å R-free 0.247
3IVQ Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-CiSBC2 Deposited 2009-09-01 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；28% PME 550, 0.1 M BTP, Cryoprotection: 35% PME 550, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.279
3IVQ Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-CiSBC2 Deposited 2009-09-01 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；28% PME 550, 0.1 M BTP, Cryoprotection: 35% PME 550, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.279
3IVV Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-PucSBC1_pep1 Deposited 2009-09-01 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；22% PME 550, 0.1 M HEPES, Cryoprotection: 30% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.199
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319
Chain C 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.263
4HS2 Crystal Structure of the Human SPOP C-terminal Domain Deposited 2012-10-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 270–374（105 aa） Fragment：C-terminal domain (UNP residues 270-374)
Mutation：L273D, L282D, L285K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；26% PEG 1500, 7% isopropanol, 0.1M CaCl2, 0.1M imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.53 Å R-free 0.151
4J8Z Crystal Structure of the Human SPOP BTB Domain Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 169–374（206 aa） Fragment：SPOP BTB domain, UNP residues 178-374
Mutation：Y353E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；32% PEG3350, 17% isopropanol, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.42 Å R-free 0.255
4J8Z Crystal Structure of the Human SPOP BTB Domain Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 169–374（206 aa） Fragment：SPOP BTB domain, UNP residues 178-374
Mutation：Y353E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；32% PEG3350, 17% isopropanol, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.42 Å R-free 0.255
4O1V SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in Kidney Cancer Deposited 2013-12-16 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：MATH domain (UNP residues 28-166)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris, 100 mM sodium malonate, 36% PEG400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.221
6F8F Co-crystal structure of SPOP MATH domain and human Pdx1 fragment Deposited 2017-12-13 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES pH 6.5, 10% (w/v) PEG6000 (final pH 7.0)
Resolution 2.00 Å R-free 0.274
6F8G Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment Deposited 2017-12-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 28–166（139 aa）
Chain B 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000
Resolution 2.03 Å R-free 0.262
6F8G Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment Deposited 2017-12-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 28–166（139 aa）
Chain D 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000
Resolution 2.03 Å R-free 0.262
6F8G Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment Deposited 2017-12-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 28–166（139 aa）
Chain D 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000
Resolution 2.03 Å R-free 0.262
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Mutation：E47K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 28–166（139 aa）
Mutation：E47K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 28–166（139 aa）
Mutation：E47K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 28–166（139 aa）
Mutation：E47K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Mutation：M117V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 28–166（139 aa）
Mutation：M117V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 28–166（139 aa）
Mutation：M117V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 28–166（139 aa）
Mutation：M117V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I7A Co-crystal structure of human SPOP MATH domain (D140N) and human BRD3 fragment Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 28–166（139 aa）
Chain E 28–166（139 aa）
Mutation：D140N Mutation：D140N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000
Resolution 2.20 Å R-free 0.234
6I7A Co-crystal structure of human SPOP MATH domain (D140N) and human BRD3 fragment Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 28–166（139 aa）
Chain G 28–166（139 aa）
Mutation：D140N Mutation：D140N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000
Resolution 2.20 Å R-free 0.234
7D3D Crystal structure of SPOP bound with a peptide Deposited 2020-09-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa） Fragment：UNP residues 28-166
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；200 mM sodium acetate trihydrate, pH 7.0, 20%(w/v) polyethylene glycol 3350
Resolution 1.45 Å R-free 0.189
7D3D Crystal structure of SPOP bound with a peptide Deposited 2020-09-18 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–166（139 aa） Fragment：UNP residues 28-166
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；200 mM sodium acetate trihydrate, pH 7.0, 20%(w/v) polyethylene glycol 3350
Resolution 1.45 Å R-free 0.189
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 29–166（138 aa） Fragment：MATH domain
Mutation：D140G PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350
Resolution 3.40 Å R-free 0.241
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 29–166（138 aa） Fragment：MATH domain
Mutation：D140G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350
Resolution 3.40 Å R-free 0.241
7LIN X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide Deposited 2021-01-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 29–166（138 aa） Fragment：MATH domain
Mutation：D140G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH was at 24 mg/ml and 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml. Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4
Resolution 1.44 Å R-free 0.186
7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 29–166（138 aa） Fragment：MATH domain
Mutation：S119D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.
Resolution 3.01 Å R-free 0.277
7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 29–166（138 aa） Fragment：MATH domain
Mutation：S119D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.
Resolution 3.01 Å R-free 0.277
7LIP X-ray structure of SPOP MATH domain (D140G) Deposited 2021-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–166（138 aa） Fragment：MATH domain
Mutation：D140G SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4. Two ul of the protein at 24 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT was mixed with 2 ul of the reservoir solution. The reservoir solution was 0.5 ml.
Resolution 1.48 Å R-free 0.205
7LIQ X-ray structure of SPOP MATH domain (S119A) Deposited 2021-01-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–166（138 aa） Fragment：MATH domain
Mutation：S119A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Crystals were grown by the hanging drop method, mixing 2 ul of the SPOP MATH S119A at 20 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.2 M (NH4)2SO4, 0.1 M BIS-Tris, pH 6.5, 25% (w/v) PEG 3,350).
Resolution 1.98 Å R-free 0.225
8DWS Full-length E47K SPOP Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Chain D 1–374（374 aa）
Chain E 1–374（374 aa）
Chain F 1–374（374 aa）
Chain G 1–374（374 aa）
Chain H 1–374（374 aa）
Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
8DWT SPOP W22R Form 2 Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 2–374（373 aa）
Chain B 2–374（373 aa）
Chain C 2–374（373 aa）
Chain D 2–374（373 aa）
Chain E 2–374（373 aa）
Chain F 2–374（373 aa）
Chain G 2–374（373 aa）
Chain H 2–374（373 aa）
Chain I 2–374（373 aa）
Chain J 2–374（373 aa）
Chain K 2–374（373 aa）
Chain L 2–374（373 aa）
Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8DWU SPOP W22R Form 1 Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Chain C 1–374（374 aa）
Chain D 1–374（374 aa）
Chain E 1–374（374 aa）
Chain F 1–374（374 aa）
Chain H 1–374（374 aa）
Chain I 1–374（374 aa）
Chain J 1–374（374 aa）
Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8DWV Full-length wild type SPOP Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–373（373 aa）
Chain B 1–373（373 aa）
Chain E 1–373（373 aa）
Chain F 1–373（373 aa）
Chain G 1–373（373 aa）
Chain H 1–373（373 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9HFV MyD88 peptide_2 bound to SPOP MATH domain Deposited 2024-11-18 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M MOPS/HEPES-Na pH 7.5
Resolution 1.45 Å R-free 0.214
9HGG SETD2 peptide bound to SPOP MATH domain Deposited 2024-11-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–166（139 aa）
Not recorded MG MAGNESIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.1 M MES/imidazole pH 6.5
Resolution 1.90 Å R-free 0.256
9OUT SPOP double donut locally refined MATH domains Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Chain C 1–374（374 aa）
Chain D 1–374（374 aa）
Chain E 1–374（374 aa）
Chain F 1–374（374 aa）
Chain G 1–374（374 aa）
Chain H 1–374（374 aa）
Chain I 1–374（374 aa）
Chain J 1–374（374 aa）
Chain K 1–374（374 aa）
Chain L 1–374（374 aa）
Chain M 1–374（374 aa）
Chain N 1–374（374 aa）
Chain P 1–374（374 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9OUU SPOP double donut locally refined MATH domains Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 1–373（373 aa）
Chain B 1–373（373 aa）
Chain C 1–373（373 aa）
Chain D 1–373（373 aa）
Chain E 1–373（373 aa）
Chain F 1–373（373 aa）
Chain G 1–373（373 aa）
Chain H 1–373（373 aa）
Chain I 1–373（373 aa）
Chain J 1–373（373 aa）
Chain K 1–373（373 aa）
Chain L 1–373（373 aa）
Chain M 1–373（373 aa）
Chain N 1–373（373 aa）
Chain P 1–373（373 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9OUW SPOP double donut locally refined MATH domains Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–373（373 aa）
Chain B 1–373（373 aa）
Chain D 1–373（373 aa）
Chain F 1–373（373 aa）
Chain H 1–373（373 aa）
Chain I 1–373（373 aa）
Chain J 1–373（373 aa）
Chain L 1–373（373 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

34 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPOP_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–145； UniProt 28–166

Bromodomain-containing protein 3

Homo sapiens

UniProt Q15059

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 245–253 Not recorded Speckle-type POZ protein × 1 （O43791） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；100 mM Tris pH 8.5, 200 mM NaCl, 25% (w/v) PEG3350 Resolution 1.90 Å R-free 0.238

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6I41 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
24OS Crystal Structure of BRD3 BD1 domain in complex with small molecule inhibitor IBET-762 Deposited 2026-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–143（120 aa） Fragment：BD1 domain
Chain B 24–143（120 aa） Fragment：BD1 domain
Not recorded EAM 2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10mM HEPES (pH 7.5),150mM NaCl, 0.5mM TCEP
Resolution 1.83 Å R-free 0.314
2E7N Solution structure of the second Bromodomain from human Bromodomain-containing protein 3 Deposited 2007-01-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–415（110 aa） Fragment：Bromodomain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.22mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O; 10% D2O | 90% H2O/10% D2O
Resolution not provided
2NXB Crystal structure of human Bromodomain containing protein 3 (BRD3) Deposited 2006-11-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–144（121 aa） Fragment：bromo 1 domain
Not recorded NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.20M KSCN, 0.1M BTPop, 20% PEG3350, 10% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.40 Å R-free 0.185
2NXB Crystal structure of human Bromodomain containing protein 3 (BRD3) Deposited 2006-11-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–144（121 aa） Fragment：bromo 1 domain
Not recorded EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.20M KSCN, 0.1M BTPop, 20% PEG3350, 10% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.40 Å R-free 0.185
2OO1 Crystal structure of the Bromo domain 2 of human Bromodomain containing protein 3 (BRD3) Deposited 2007-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 307–416（110 aa） Fragment：Bromo 2 Domain
Not recorded NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M NaF, 0.1M BTProp, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.70 Å R-free 0.213
2OO1 Crystal structure of the Bromo domain 2 of human Bromodomain containing protein 3 (BRD3) Deposited 2007-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 307–416（110 aa） Fragment：Bromo 2 Domain
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M NaF, 0.1M BTProp, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.70 Å R-free 0.213
2OO1 Crystal structure of the Bromo domain 2 of human Bromodomain containing protein 3 (BRD3) Deposited 2007-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 307–416（110 aa） Fragment：Bromo 2 Domain
Not recorded 7PE 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M NaF, 0.1M BTProp, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.70 Å R-free 0.213
2OO1 Crystal structure of the Bromo domain 2 of human Bromodomain containing protein 3 (BRD3) Deposited 2007-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 307–416（110 aa） Fragment：Bromo 2 Domain
Not recorded NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M NaF, 0.1M BTProp, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.70 Å R-free 0.213
2YW5 Solution structure of the bromodomain from human bromodomain containing protein 3 Deposited 2007-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–155（131 aa） Fragment：UNP residues 25-155, bromodomain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.2mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3S91 Crystal Structure of the first bromodomain of human BRD3 in complex with the inhibitor JQ1 Deposited 2011-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–144（121 aa）
Not recorded JQ1 (6S)-6-(2-tert-butoxy-2-oxoethyl)-4-(4-chlorophenyl)-2,3,9-trimethyl-6,7-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium × 2 IPA ISOPROPYL ALCOHOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；14% isopropanol, 0.14M CaCl2, 30% glycerol, 0.7M acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.06 Å R-free 0.233
3S92 Crystal Structure of the second bromodomain of human BRD3 in complex with the inhibitor JQ1 Deposited 2011-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–416（111 aa）
Not recorded JQ1 (6S)-6-(2-tert-butoxy-2-oxoethyl)-4-(4-chlorophenyl)-2,3,9-trimethyl-6,7-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M (NH4)2Hcit, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.36 Å R-free 0.186
5A7C Crystal structure of the second bromodomain of human BRD3 in complex with compound Deposited 2015-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–416（111 aa） Fragment：BROMO 2 DOMAIN, RESIDUES 306-416
Not recorded 5D4 N-(6-ACETAMIDOHEXYL)ACETAMIDE × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；19% PEG 6000, 0.1M HEPES PH 7.0
Resolution 1.90 Å R-free 0.256
5A7C Crystal structure of the second bromodomain of human BRD3 in complex with compound Deposited 2015-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 306–416（111 aa） Fragment：BROMO 2 DOMAIN, RESIDUES 306-416
Not recorded 5D4 N-(6-ACETAMIDOHEXYL)ACETAMIDE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；19% PEG 6000, 0.1M HEPES PH 7.0
Resolution 1.90 Å R-free 0.256
5A7C Crystal structure of the second bromodomain of human BRD3 in complex with compound Deposited 2015-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 306–416（111 aa） Fragment：BROMO 2 DOMAIN, RESIDUES 306-416
Not recorded 5D4 N-(6-ACETAMIDOHEXYL)ACETAMIDE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；19% PEG 6000, 0.1M HEPES PH 7.0
Resolution 1.90 Å R-free 0.256
5A7C Crystal structure of the second bromodomain of human BRD3 in complex with compound Deposited 2015-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 306–416（111 aa） Fragment：BROMO 2 DOMAIN, RESIDUES 306-416
Not recorded 5D4 N-(6-ACETAMIDOHEXYL)ACETAMIDE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；19% PEG 6000, 0.1M HEPES PH 7.0
Resolution 1.90 Å R-free 0.256
5HFR Crystal structure of the second bromodomain H395R mutant of human BRD3 Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–416（111 aa） Fragment：UNP residues 306-416
Mutation：H395R NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium nitrate, 10 % PEG 3350, 5 % EDO, 0.1 M bis tris prop. pH 6.5
Resolution 1.70 Å R-free 0.221
5HFR Crystal structure of the second bromodomain H395R mutant of human BRD3 Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 306–416（111 aa） Fragment：UNP residues 306-416
Mutation：H395R EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium nitrate, 10 % PEG 3350, 5 % EDO, 0.1 M bis tris prop. pH 6.5
Resolution 1.70 Å R-free 0.221
5HFR Crystal structure of the second bromodomain H395R mutant of human BRD3 Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 306–416（111 aa） Fragment：UNP residues 306-416
Mutation：H395R EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium nitrate, 10 % PEG 3350, 5 % EDO, 0.1 M bis tris prop. pH 6.5
Resolution 1.70 Å R-free 0.221
5HFR Crystal structure of the second bromodomain H395R mutant of human BRD3 Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 306–416（111 aa） Fragment：UNP residues 306-416
Mutation：H395R EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium nitrate, 10 % PEG 3350, 5 % EDO, 0.1 M bis tris prop. pH 6.5
Resolution 1.70 Å R-free 0.221
5HJC BRD3 second bromodomain in complex with histone H3 acetylation at K18 Deposited 2016-01-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 307–416（110 aa） Fragment：second bromodomain, UNP residues 307-416
Not recorded EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30%(w/v) polyethylene glycol methyl ether 5000, 0.2 M ammonium sulfate, 0.1 M MES, 0.1 M guanidine hydrochloride
Resolution 2.60 Å R-free 0.269
6BGG Solution NMR structures of the BRD3 ET domain in complex with a CHD4 peptide Deposited 2017-10-28 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 557–644（88 aa） Fragment：unp residues 557-644
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) .2；Pressure 1
NMR sample composition 500 uM [U-13C; U-15N] BRD3, 500 uM CHD4, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 uM [U-13C; U-15N] BRD3, 500 uM CHD4, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 100% D2O | 100% D2O
NMR sample composition 500 uM BRD3, 500 uM CHD4, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6BGH Solution NMR structure of Brd3 ET domain bound to Brg1 peptide Deposited 2017-10-28 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 557–643（87 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50 NaCl；Pressure 1
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50 NaCl；Pressure 1
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50 NaCl；Pressure 1
NMR sample composition 300 uM Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 300 uM [U-15N] Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 300 uM [U-13C; U-15N] Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14 Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350
Resolution 1.81 Å R-free 0.227
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15 Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.237
6I7A Co-crystal structure of human SPOP MATH domain (D140N) and human BRD3 fragment Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 245–253（9 aa）
Chain F 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000
Resolution 2.20 Å R-free 0.234
6I7A Co-crystal structure of human SPOP MATH domain (D140N) and human BRD3 fragment Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 245–253（9 aa）
Chain H 245–253（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000
Resolution 2.20 Å R-free 0.234
6QJU Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with 3-bromo-1H-indazol-5-amine Deposited 2019-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–144（121 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 SCN THIOCYANATE ION × 1 J58 3-bromanyl-2~{H}-indazol-5-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.20 M KSCN, 0.1 M BTPop, 20% PEG3350, 10% EtGly, soaked with 14% DMSO containing 42mM 3-bromo-1H-imidazol-5-amine
Resolution 1.20 Å R-free 0.160
6QJU Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with 3-bromo-1H-indazol-5-amine Deposited 2019-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–144（121 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.20 M KSCN, 0.1 M BTPop, 20% PEG3350, 10% EtGly, soaked with 14% DMSO containing 42mM 3-bromo-1H-imidazol-5-amine
Resolution 1.20 Å R-free 0.160
6U4A BRD3-BD1 in complex with the cyclic peptide 3.1_3 Deposited 2019-08-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–147（123 aa）
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium sulfate 0.1 M Bis-Tris propane 8.5 20 % w/v PEG 3350
Resolution 1.88 Å R-free 0.188
6U4A BRD3-BD1 in complex with the cyclic peptide 3.1_3 Deposited 2019-08-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–147（123 aa）
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium sulfate 0.1 M Bis-Tris propane 8.5 20 % w/v PEG 3350
Resolution 1.88 Å R-free 0.188
6ULP BRD3-BD2 in complex with the cyclic peptide 3.2_3 Deposited 2019-10-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 307–419（113 aa） Fragment：second bromodomain
Chain B 307–419（113 aa） Fragment：second bromodomain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.2 M Calcium chloride dihydrate, 0.1 M Tris 8.0, 20 % w/v PEG 6000
Resolution 2.80 Å R-free 0.248
7JMY Solution NMR structure of human Brd3 ET domain Deposited 2020-08-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 554–640（87 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1
NMR sample composition 0.5 mM [U-15N] Brd3 ET Domain, 100 mM sodium chloride, 20 mM Na3PO4, 2 mM 2-mercapto ethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-13C; U-15N] Brd3 ET Domain, 100 mM sodium chloride, 20 mM Na3PO4, 2 mM beta-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7JQ8 Solution NMR structure of human Brd3 ET domain Deposited 2020-08-10 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 554–640（87 aa） Fragment：NET domain, residues 554-640
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] MLV IN TP, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] Brd3 ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM Brd3 ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM Brd3 ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7JYN Solution NMR structure of human Brd3 ET complexed with NSD3(148-184) peptide Deposited 2020-08-31 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 554–640（87 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] NSD3(148-184), 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.25 mM NSD3(148-184), 0.25 mM U-100% 13C; U-100% 15 Brd3ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.25 mM [U-100% 13C; U-100% 15N] NSD3(148-184), 0.2 mM [U-100% 13C; U-100% 15N] Brd3ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7JYZ Solution NMR structure and dynamics of human Brd3 ET in complex with MLV IN CTD Deposited 2020-09-01 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 554–640（87 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR sample composition 0.25 mM [U-100% 13C; U-100% 15N] Brd3 ET, 0.25 mM [U-100% 13C; U-100% 15N] MLV-IN-CTD, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.25 mM [U-15N] Brd3 ET, 0.25 mM [U-15N] MLV-IN-CTD, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7L72 Crystal structure of the second bromodomain (BD2) of human BRD3 bound to Ro3280 Deposited 2020-12-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–416（111 aa）
Not recorded 79C 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M L-Proline, 0.1 M HEPES pH 7.5, 10 % w/v Polyethylene glycol 3,350
Resolution 1.50 Å R-free 0.182
7L9L Crystal structure of the second bromodomain (BD2) of human BRD3 bound to BI2536 Deposited 2021-01-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–416（111 aa）
Not recorded R78 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 10 % w/v Polyethylene glycol 6,000, 5 % v/v (+/-)-2-Methyl-2,4-pentanediol
Resolution 1.55 Å R-free 0.178
7LAY Crystal structure of the first bromodomain (BD1) of human BRD3 bound to SG3-179 Deposited 2021-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–144（121 aa）
Not recorded 5W2 4-[[4-[[3-(~{tert}-butylsulfonylamino)-4-chloranyl-phenyl]amino]-5-methyl-pyrimidin-2-yl]amino]-2-fluoranyl-~{N}-(1-methylpiperidin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 3,350
Resolution 1.45 Å R-free 0.188
7LAY Crystal structure of the first bromodomain (BD1) of human BRD3 bound to SG3-179 Deposited 2021-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–144（121 aa）
Not recorded 5W2 4-[[4-[[3-(~{tert}-butylsulfonylamino)-4-chloranyl-phenyl]amino]-5-methyl-pyrimidin-2-yl]amino]-2-fluoranyl-~{N}-(1-methylpiperidin-4-yl)benzamide × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 3,350
Resolution 1.45 Å R-free 0.188
7LAZ Crystal structure of the first bromodomain (BD1) of human BRD3 bound to ERK5-IN-1 Deposited 2021-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–144（121 aa）
Not recorded VYJ 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 4.3 M Sodium chloride
Resolution 2.30 Å R-free 0.240
7LAZ Crystal structure of the first bromodomain (BD1) of human BRD3 bound to ERK5-IN-1 Deposited 2021-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–144（121 aa）
Not recorded VYJ 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 4.3 M Sodium chloride
Resolution 2.30 Å R-free 0.240
7LB4 Crystal structure of the second bromodomain (BD2) of human BRD3 bound to bromosporine Deposited 2021-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–416（111 aa）
Not recorded BMF Bromosporine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 10 % w/v Polyethylene glycol 6,000, 5 % v/v (+/-)-2-Methyl-2,4-pentanediol
Resolution 2.00 Å R-free 0.229
7LB4 Crystal structure of the second bromodomain (BD2) of human BRD3 bound to bromosporine Deposited 2021-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 306–416（111 aa）
Not recorded BMF Bromosporine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 10 % w/v Polyethylene glycol 6,000, 5 % v/v (+/-)-2-Methyl-2,4-pentanediol
Resolution 2.00 Å R-free 0.229
7LBT Crystal structure of the second bromodomain (BD2) of human BRD3 bound to ERK5-IN-1 Deposited 2021-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–416（111 aa）
Not recorded VYJ 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol, 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1MBuffer System 3 (pH 8.5 Tris (base) and BICINE 1.0M each), 37.5% v/vPrecipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Resolution 2.70 Å R-free 0.232
7LBT Crystal structure of the second bromodomain (BD2) of human BRD3 bound to ERK5-IN-1 Deposited 2021-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 306–416（111 aa）
Not recorded VYJ 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol, 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1MBuffer System 3 (pH 8.5 Tris (base) and BICINE 1.0M each), 37.5% v/vPrecipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Resolution 2.70 Å R-free 0.232
7LBT Crystal structure of the second bromodomain (BD2) of human BRD3 bound to ERK5-IN-1 Deposited 2021-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 306–416（111 aa）
Not recorded VYJ 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol, 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1MBuffer System 3 (pH 8.5 Tris (base) and BICINE 1.0M each), 37.5% v/vPrecipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Resolution 2.70 Å R-free 0.232
7LBT Crystal structure of the second bromodomain (BD2) of human BRD3 bound to ERK5-IN-1 Deposited 2021-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 306–416（111 aa）
Not recorded VYJ 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol, 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1MBuffer System 3 (pH 8.5 Tris (base) and BICINE 1.0M each), 37.5% v/vPrecipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Resolution 2.70 Å R-free 0.232
7R8R Physachenolide C with Bromodomain (BRD3-BD1) Deposited 2021-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–144（121 aa）
Not recorded 8L6 Physachenolide C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10mM CaCl, 50mM Tris-HCl pH 8.5, 30% w/v PEG 4000
Resolution 1.80 Å R-free 0.235
7RJK Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with hnRNPK Deposited 2021-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–144（121 aa） Fragment：UNP residues 24-144
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；2.0 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.2 M potassium/sodium tartrate tetrahydrate
Resolution 1.85 Å R-free 0.217
7RJK Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with hnRNPK Deposited 2021-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–144（121 aa） Fragment：UNP residues 24-144
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；2.0 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.2 M potassium/sodium tartrate tetrahydrate
Resolution 1.85 Å R-free 0.217
7RJL Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT Deposited 2021-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–144（121 aa） Fragment：UNP residues 24-144
Not recorded EDO 1,2-ETHANEDIOL × 6 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；35% v/v Tacsimate
Resolution 1.50 Å R-free 0.185
7RJL Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT Deposited 2021-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–144（121 aa） Fragment：UNP residues 24-144
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；35% v/v Tacsimate
Resolution 1.50 Å R-free 0.185
7RJM Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with ILF3 Deposited 2021-07-21 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–144（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；292 K；25% w/v PEG3350, 0.1 M Bis-Tris, 0.2 M sodium chloride
Resolution 2.10 Å R-free 0.237
7RJM Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with ILF3 Deposited 2021-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–144（121 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；292 K；25% w/v PEG3350, 0.1 M Bis-Tris, 0.2 M sodium chloride
Resolution 2.10 Å R-free 0.237
7RJN Crystal structure of human bromodomain containing protein 3 (BRD3) in complex with BCLTF1 Deposited 2021-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–144（121 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；292 K；0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, 30% w/v PEG4000
Resolution 1.95 Å R-free 0.234
7RJN Crystal structure of human bromodomain containing protein 3 (BRD3) in complex with BCLTF1 Deposited 2021-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–144（121 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；292 K；0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, 30% w/v PEG4000
Resolution 1.95 Å R-free 0.234
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain K 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7S3P BD2 domain of human BRD3 bound to Physachenolide C Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 306–416（111 aa）
Not recorded 8L6 Physachenolide C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240
7TO7 BRD3-BD1 in complex with RaPID linear peptide 1xAcK.4XE (monoAcK.4xE) Deposited 2022-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Chain B 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M PCTP, pH 4.0, 25% w/v PEG1500
Resolution 1.93 Å R-free 0.251
7TO7 BRD3-BD1 in complex with RaPID linear peptide 1xAcK.4XE (monoAcK.4xE) Deposited 2022-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Chain E 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M PCTP, pH 4.0, 25% w/v PEG1500
Resolution 1.93 Å R-free 0.251
7TO8 BRD3-BD1 in complex with RaPID linear peptide 2xAcK.1 (diAcK.1) Deposited 2022-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Chain B 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MMT, pH 6.0, 25% w/v PEG1500
Resolution 1.50 Å R-free 0.200
7TO9 BRD3-BD1 in complex with RaPID linear peptide 2xAcK.4xE (diAcK.4xE) Deposited 2022-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–147（123 aa）
Chain B 25–147（123 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES, pH 7.5, 0.2 M sodium chloride, 10% v/v 2-propanol
Resolution 1.60 Å R-free 0.227
7TOA BRD3-BD1 in complex with RaPID linear peptide 3xAcK.1 (triAcK.1) Deposited 2022-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 32–147（116 aa） Fragment：BD1 (UNP residues 32-147)
Chain B 32–147（116 aa） Fragment：BD1 (UNP residues 32-147)
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350
Resolution 1.41 Å R-free 0.196
7UG5 Second bromodomain of BRD3 liganded with BMS-536924 Deposited 2022-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 306–416（111 aa）
Not recorded N6I (3M)-4-{[(2S)-2-(3-chlorophenyl)-2-hydroxyethyl]amino}-3-[4-methyl-6-(morpholin-4-yl)-1H-benzimidazol-2-yl]pyridin-2(1H)-one × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH7.5, 30% v/v Polyethylene glycol monomethyl ether 550
Resolution 1.80 Å R-free 0.224
7UG5 Second bromodomain of BRD3 liganded with BMS-536924 Deposited 2022-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 306–416（111 aa）
Not recorded N6I (3M)-4-{[(2S)-2-(3-chlorophenyl)-2-hydroxyethyl]amino}-3-[4-methyl-6-(morpholin-4-yl)-1H-benzimidazol-2-yl]pyridin-2(1H)-one × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH7.5, 30% v/v Polyethylene glycol monomethyl ether 550
Resolution 1.80 Å R-free 0.224
7UG5 Second bromodomain of BRD3 liganded with BMS-536924 Deposited 2022-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 306–416（111 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH7.5, 30% v/v Polyethylene glycol monomethyl ether 550
Resolution 1.80 Å R-free 0.224
7UG5 Second bromodomain of BRD3 liganded with BMS-536924 Deposited 2022-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 306–416（111 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH7.5, 30% v/v Polyethylene glycol monomethyl ether 550
Resolution 1.80 Å R-free 0.224
8B5A Human BRD3 bromodomain 2 in complex with a H4 peptide containing ApmTri (H4K20ApmTri) Deposited 2022-09-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 307–416（110 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM potassium sodium tatrate 100 mM sodium citrate pH 5.6 2 M ammonium sulfate
Resolution 1.92 Å R-free 0.250
8CV5 Peptide 4.2B in complex with BRD3.2 Deposited 2022-05-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 307–419（113 aa） Fragment：BD2 (UNP residues 307-419)
Not recorded ACE ACETYL GROUP × 1 NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium sulfate, 20% w/v PEG3350
Resolution 1.47 Å R-free 0.197
9MPF BRD3-BD1 in complex with cyclic peptide 2.1B Deposited 2024-12-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Lithium sulfate, 0.1 M Phosphate/citrate pH 4.2, 20 % w/v PEG 1000
Resolution 2.70 Å R-free 0.219
9MPH BRD3-BD1 in complex with cyclic peptide 4.1D Deposited 2024-12-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Chain D 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M lithium chloride pH 6.8, 20% (w/v) PEG3350
Resolution 2.25 Å R-free 0.249
9MPH BRD3-BD1 in complex with cyclic peptide 4.1D Deposited 2024-12-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Chain C 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M lithium chloride pH 6.8, 20% (w/v) PEG3350
Resolution 2.25 Å R-free 0.249
9MPK BRD3-BD1 in complex with cyclic peptide 2.1C-Y5A Deposited 2024-12-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium citrate pH 5.5, 20 % w/v PEG 3000
Resolution 2.70 Å R-free 0.295
9MPK BRD3-BD1 in complex with cyclic peptide 2.1C-Y5A Deposited 2024-12-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium citrate pH 5.5, 20 % w/v PEG 3000
Resolution 2.70 Å R-free 0.295
9MPK BRD3-BD1 in complex with cyclic peptide 2.1C-Y5A Deposited 2024-12-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium citrate pH 5.5, 20 % w/v PEG 3000
Resolution 2.70 Å R-free 0.295
9MPK BRD3-BD1 in complex with cyclic peptide 2.1C-Y5A Deposited 2024-12-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium citrate pH 5.5, 20 % w/v PEG 3000
Resolution 2.70 Å R-free 0.295
9MPK BRD3-BD1 in complex with cyclic peptide 2.1C-Y5A Deposited 2024-12-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium citrate pH 5.5, 20 % w/v PEG 3000
Resolution 2.70 Å R-free 0.295
9MPK BRD3-BD1 in complex with cyclic peptide 2.1C-Y5A Deposited 2024-12-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium citrate pH 5.5, 20 % w/v PEG 3000
Resolution 2.70 Å R-free 0.295
9MPM BRD3-BD1 in complex with cyclic peptide 2.1C-W11A Deposited 2024-12-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
Resolution 2.60 Å R-free 0.263
9MPM BRD3-BD1 in complex with cyclic peptide 2.1C-W11A Deposited 2024-12-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–147（123 aa） Fragment：BD1 (UNP residues 25-147)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
Resolution 2.60 Å R-free 0.263
9MPN BRD3-BD1 A128T mutant Deposited 2024-12-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–147（123 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Calcium chloride dihydrate, 0.1 M BIS-Tris pH 5.5, 45 % v/v MPD
Resolution 1.60 Å R-free 0.210
9MPN BRD3-BD1 A128T mutant Deposited 2024-12-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 25–147（123 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Calcium chloride dihydrate, 0.1 M BIS-Tris pH 5.5, 45 % v/v MPD
Resolution 1.60 Å R-free 0.210
9MPN BRD3-BD1 A128T mutant Deposited 2024-12-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 25–147（123 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Calcium chloride dihydrate, 0.1 M BIS-Tris pH 5.5, 45 % v/v MPD
Resolution 1.60 Å R-free 0.210
9MPN BRD3-BD1 A128T mutant Deposited 2024-12-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 25–147（123 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Calcium chloride dihydrate, 0.1 M BIS-Tris pH 5.5, 45 % v/v MPD
Resolution 1.60 Å R-free 0.210
9NN4 BET BRD3-BD1 in complex with peptide 7.2 Deposited 2025-03-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–147（120 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 7.0 PEG 8000
Resolution 1.37 Å R-free 0.195
9NN4 BET BRD3-BD1 in complex with peptide 7.2 Deposited 2025-03-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–147（120 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 7.0 PEG 8000
Resolution 1.37 Å R-free 0.195

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View Construct and Data Evidence
UniProt name BRD3_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–9； UniProt 245–253

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6i41

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6i41
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6i41
Deposition date deposition_date2018-11-08
Structure title titleCo-crystal structure of human SPOP MATH domain (wild-type) and human BRD3 fragment
Keywords keywordsligase nuclear cancer ubiquitination, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.60 Å
Radius of gyration Rg (electron density) rg_electron15.14 Å
Forward intensity I(0) i04740210.00
Molecular weight molecular_weight15889.0 kDa
Excluded volume excluded_volume19984 ų
Envelope volume envelope_volume22626 ų
Hydration-shell volume shell_volume12897 ų
Envelope diameter envelope_diameter56.6 Å
Shell Rg shell_rg20.77 Å
Envelope Rg envelope_rg15.62 Å
Shape Rg shape_rg15.11 Å
Total Rg total_rg16.33 Å
Total atoms total_atoms1120
Residues n_residues147
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.2 Å
Rg (real space) rg_real16.57 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real4.7400e+06
I(0) uncertainty (real space) i0_real_error5.9800e+04
Rg (reciprocal space) rg_reciprocal16.57 Å
I(0) (reciprocal space) i0_reciprocal4740000.0000
Solution quality estimate total_estimate0.8634
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.3 Å
Skewness Skewness skewness0.308
Kurtosis Kurtosis kurtosis-0.255
Angular range angular_range— – 0.4800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha926200.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.987
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6i41a1
Class classb — All beta proteins
Fold Fold foldb.8 — TRAF domain-like
Superfamily Superfamily superfamilyb.8.1 — TRAF domain-like
Family Family familyb.8.1.1 — MATH domain
Domain ID domain_idd6i41a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id6i41A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
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8. Citations (1)

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9. Files and Curves (10)