9mph

BRD3-BD1 in complex with cyclic peptide 4.1D

Method: X-RAY DIFFRACTION D_max: 92.5 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Bromodomain-containing protein 3

Homo sapiens

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 25–147 Chain D； UniProt 25–147	Fragment：BD1 (UNP residues 25-147)	4.1D × 1	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 25–147 Chain C； UniProt 25–147	Fragment：BD1 (UNP residues 25-147)	4.1D × 1	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

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 9MPH	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 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 mutation/modification 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 24–144（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 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）	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 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：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 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：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 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：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 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：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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
6I41 Co-crystal structure of human SPOP MATH domain (wild-type) and human BRD3 fragment Deposited 2018-11-08	Different construct Different mutation/modification Different oligomeric state 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；100 mM Tris pH 8.5, 200 mM NaCl, 25% (w/v) PEG3350	Resolution 1.90 Å R-free 0.238
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14	Different construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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）	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 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）	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 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 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 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 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 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 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 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 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 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）	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 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）	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 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）	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 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）	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 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）	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 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）	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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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 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）	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 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）	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 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）	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 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）	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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
9MPK BRD3-BD1 in complex with cyclic peptide 2.1C-Y5A 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 × 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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

47 other PDB entries and 100 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BRD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–128； UniProt 25–147 Author chain B； PDBConstruct 6–128； UniProt 25–147 Author chain C； PDBConstruct 6–128； UniProt 25–147 Author chain D； PDBConstruct 6–128； UniProt 25–147

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9mph
Deposition date deposition_date	2024-12-30
最后修订 last_revision	2026-04-08
Structure title title	BRD3-BD1 in complex with cyclic peptide 4.1D
Keywords keywords	BRD3, cyclic peptide, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.18 Å
Radius of gyration Rg (electron density) rg_electron	26.67 Å
Forward intensity I(0) i0	55995300.00
Molecular weight molecular_weight	60407.0 kDa
Excluded volume excluded_volume	76428 Å³
Envelope volume envelope_volume	93269 Å³
Hydration-shell volume shell_volume	29842 Å³
Envelope diameter envelope_diameter	101.1 Å
Shell Rg shell_rg	33.00 Å
Envelope Rg envelope_rg	27.00 Å
Shape Rg shape_rg	26.67 Å
Total Rg total_rg	27.35 Å
Total atoms total_atoms	4243
Residues n_residues	500
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	92.5 Å
Rg (real space) rg_real	27.26 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	5.6000e+07
I(0) uncertainty (real space) i0_real_error	8.1560e+05
Rg (reciprocal space) rg_reciprocal	27.24 Å
I(0) (reciprocal space) i0_reciprocal	55990000.0000
Solution quality estimate total_estimate	0.7981
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	30.3 Å
Skewness Skewness skewness	0.441
Kurtosis Kurtosis kurtosis	-0.219
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15750000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Bromodomain-containing protein 3
Molecular weight formula_weight	15095.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4352

QPLGSEVSNPSKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEEVEL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	4.1D
Molecular weight formula_weight	2010.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

XWKSLRGRKFLTKYLCX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	109

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8. Citations (1)

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Unit-cell length a length_a	45.703 Å
Unit-cell length b length_b	135.549 Å
Unit-cell length c length_c	109.094 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	42.180 Å
R factor r_factor	0.2174
R_work r_work	0.2152
R_free r_free	0.2491

fit	/app/data/saxs_computation/mp/9mph/9mph.fit
pddf	/app/data/pr_computation/mp/9mph/9mph.pr.out
profile	/app/data/saxs_computation/mp/9mph/9mph.dat

BRD3-BD1 in complex with cyclic peptide 4.1D

1. Protein Identity and Related Structures Protein Identity & Related Structures

Bromodomain-containing protein 3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)