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7jyn

Solution NMR structure of human Brd3 ET complexed with NSD3(148-184) peptide

Method: SOLUTION NMR Dmax: 49.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 A； UniProt 554–640 Not recorded Histone-lysine N-methyltransferase NSD3 × 1 （Q9BZ95） 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

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 7JYN 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 method 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 conditions 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 method 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 method 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 method 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 method 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 method 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 method 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 conditions 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 conditions 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 conditions 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 oligomeric state Different experimental conditions 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 conditions 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
7JYZ Solution NMR structure and dynamics of human Brd3 ET in complex with MLV IN CTD Deposited 2020-09-01 Different experimental conditions 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 101 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 10–96； UniProt 554–640

Histone-lysine N-methyltransferase NSD3

Homo sapiens

UniProt Q9BZ95

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 148–184 Not recorded Bromodomain-containing protein 3 × 1 （Q15059） 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

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 7JYN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2DAQ Solution structure of second PWWP domain of WHSC1L1 protein Deposited 2005-12-14 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 957–1053（97 aa） Fragment：PWWP domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient
NMR sample composition 0.60mM PWWP domain; U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2NCZ Solution NMR structures of BRD4 ET domain in complex with NSD3_1 peptide Deposited 2016-04-18 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 152–163（12 aa） Fragment：residues 152-163
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2ND1 Solution NMR structures of BRD4 ET domain in complex with NSD3_3 peptide Deposited 2016-04-19 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 593–605（13 aa） Fragment：residues 593-605
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
4GND Crystal Structure of NSD3 tandem PHD5-C5HCH domains Deposited 2012-08-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；0.1M Hepes, 1.1M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.27 Å R-free 0.219
4GND Crystal Structure of NSD3 tandem PHD5-C5HCH domains Deposited 2012-08-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；0.1M Hepes, 1.1M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.27 Å R-free 0.219
4GNE Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7 Deposited 2012-08-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；0.1M Tris-HCl pH 7.0, 30% (w/v) PEG 3000, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.47 Å R-free 0.178
4GNF Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15 Deposited 2012-08-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.55 Å R-free 0.205
4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413
Not recorded ZN ZINC ION × 4 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.73 Å R-free 0.214
4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.73 Å R-free 0.214
4RXJ crystal structure of WHSC1L1-PWWP2 Deposited 2014-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 953–1064（112 aa）
Not recorded UNX UNKNOWN LIGAND × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 3.5；293 K；25% w/v PEG3350, 10% citric acid, pH 3.5, vapor diffusion, temperature 293K, VAPOR DIFFUSION
Resolution 2.10 Å R-free 0.272
5UPD Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1) Deposited 2017-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1054–1285（232 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 UNX UNKNOWN LIGAND × 17 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG-5000-MME, 0.1 M bis-tris, 0.02 M sarcosine
Resolution 1.80 Å R-free 0.218
6CEN Crystal Structure of WHSC1L1 in Complex with Inhibitor PEP21 Deposited 2018-02-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1058–1285（228 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1 M Bis-Tris pH 6.5, 20% w/v PEG5000MME
Resolution 1.61 Å R-free 0.215
6G24 X-ray structure of NSD3-PWWP1 in complex with compound 3 Deposited 2018-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 263–398（136 aa）
Not recorded EH2 2-[(~{E})-2-thiophen-2-ylethenyl]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Resolution 2.10 Å R-free 0.235
6G25 X-ray structure of NSD3-PWWP1 in complex with compound 4 Deposited 2018-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 263–398（136 aa）
Not recorded EHQ 3,5-dimethyl-4-(4-pyridin-4-yl-1~{H}-pyrazol-3-yl)-1,2-oxazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Resolution 1.43 Å R-free 0.229
6G27 X-ray structure of NSD3-PWWP1 in complex with compound 5 Deposited 2018-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 263–398（136 aa）
Not recorded EHE 5-methyl-6-phenyl-2-piperidin-4-yl-pyridazin-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Resolution 1.65 Å R-free 0.227
6G29 X-ray structure of NSD3-PWWP1 in complex with compound 6 Deposited 2018-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 263–398（136 aa）
Not recorded EHK 5-methyl-2-piperidin-4-yl-6-pyridin-4-yl-pyridazin-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Resolution 1.70 Å R-free 0.210
6G2B X-ray structure of NSD3-PWWP1 in complex with compound 8 Deposited 2018-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 263–398（136 aa）
Not recorded EH8 4-(3-methyl-5-phenyl-imidazol-4-yl)pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Resolution 1.61 Å R-free 0.225
6G2C X-ray structure of NSD3-PWWP1 in complex with compound 9 Deposited 2018-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 263–398（136 aa）
Not recorded EHT 3,5-dimethyl-4-(1-methyl-5-pyridin-4-yl-imidazol-4-yl)-1,2-oxazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Resolution 1.76 Å R-free 0.230
6G2E X-ray structure of NSD3-PWWP1 in complex with compound 13 Deposited 2018-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 263–398（136 aa）
Not recorded EHH [3,5-dimethyl-4-(1-methyl-5-pyridin-4-yl-imidazol-4-yl)phenyl]methanamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Resolution 1.85 Å R-free 0.252
6G2F X-ray structure of NSD3-PWWP1 in complex with compound 16 Deposited 2018-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 263–398（136 aa）
Not recorded EHW 4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-1,2-oxazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Resolution 1.74 Å R-free 0.211
6G2O X-ray structure of NSD3-PWWP1 in complex with compound BI-9321 Deposited 2018-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 263–398（136 aa）
Not recorded EJE [4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-phenyl]methanamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Resolution 1.81 Å R-free 0.224
6G3P X-ray structure of seleno-methionine labelled NSD3-PWWP1 Deposited 2018-03-26 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 247–398（152 aa） Fragment：UNP residues 247-398
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；293 K；50 mM TRIS pH 9.0, 23% PEG3350
Resolution 2.80 Å R-free 0.262
6G3P X-ray structure of seleno-methionine labelled NSD3-PWWP1 Deposited 2018-03-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 247–398（152 aa） Fragment：UNP residues 247-398
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；293 K；50 mM TRIS pH 9.0, 23% PEG3350
Resolution 2.80 Å R-free 0.262
6G3P X-ray structure of seleno-methionine labelled NSD3-PWWP1 Deposited 2018-03-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 247–398（152 aa） Fragment：UNP residues 247-398
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；293 K；50 mM TRIS pH 9.0, 23% PEG3350
Resolution 2.80 Å R-free 0.262
6G3P X-ray structure of seleno-methionine labelled NSD3-PWWP1 Deposited 2018-03-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 247–398（152 aa） Fragment：UNP residues 247-398
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；293 K；50 mM TRIS pH 9.0, 23% PEG3350
Resolution 2.80 Å R-free 0.262
6G3T X-ray structure of NSD3-PWWP1 Deposited 2018-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 247–398（152 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol
Resolution 2.53 Å R-free 0.274
6G3T X-ray structure of NSD3-PWWP1 Deposited 2018-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 247–398（152 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol
Resolution 2.53 Å R-free 0.274
6G3T X-ray structure of NSD3-PWWP1 Deposited 2018-03-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 247–398（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol
Resolution 2.53 Å R-free 0.274
6G3T X-ray structure of NSD3-PWWP1 Deposited 2018-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 247–398（152 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol
Resolution 2.53 Å R-free 0.274
7CRP NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode) Deposited 2020-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain I 680–1437（758 aa）
Mutation：E1181K, T1232A SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7CRQ NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) Deposited 2020-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain I 680–1437（758 aa）
Chain L 680–1437（758 aa）
Mutation：E1181K, T1232A Mutation：E1181K, T1232A SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.15 Å
7CRR Native NSD3 bound to 187-bp nucleosome Deposited 2020-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain I 680–1437（758 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.48 Å

24 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NSD3_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–39； UniProt 148–184

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 7jyn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7jyn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7jyn
Deposition date deposition_date2020-08-31
Structure title titleSolution NMR structure of human Brd3 ET complexed with NSD3(148-184) peptide
Keywords keywordsBrd3 ET, NSD3 solution NMR, Integrase, extra terminal domain, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.95 Å
Radius of gyration Rg (electron density) rg_electron24.43 Å
Forward intensity I(0) i01512610000.00
Molecular weight molecular_weight310870.0 kDa
Excluded volume excluded_volume382680 ų
Envelope volume envelope_volume191660 ų
Hydration-shell volume shell_volume42005 ų
Envelope diameter envelope_diameter147.5 Å
Shell Rg shell_rg41.34 Å
Envelope Rg envelope_rg43.81 Å
Shape Rg shape_rg24.61 Å
Total Rg total_rg24.28 Å
Total atoms total_atoms43340
Residues n_residues2700
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 dmax49.9 Å
Rg (real space) rg_real17.87 Å
Rg uncertainty (real space) rg_real_error0.09 Å
I(0) (real space) i0_real1.2440e+09
I(0) uncertainty (real space) i0_real_error1.3650e+07
Rg (reciprocal space) rg_reciprocal26.10 Å
I(0) (reciprocal space) i0_reciprocal1512000000.0000
Solution quality estimate total_estimate0.6064
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary19.8 Å
Skewness Skewness skewness0.363
Kurtosis Kurtosis kurtosis-0.437
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha4.2860
Highest regularization parameter α highest_alpha1193000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.054; Oscil: 0.985; Stabil: 0.976; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7jynA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily220 —
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8. Citations (1)

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9. Files and Curves (10)