6aze

Crystal Structure of the BPTF PHD-bromodomain module bound to H3KC4me3 methyl lysine analog

Method: X-RAY DIFFRACTION D_max: 82.7 Å Quality: REASONABLE

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

Nucleosome-remodeling factor subunit BPTF

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2866–3032	Fragment：PHD-bromodomain	ALA-ARG-THR-ML3-GLN-THR × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1uL complex solution (~8 mg/ml of [1:1.2 protein to peptide molar ratio] in 100 mM KCl, 10 mM HEPES KOH, pH 7.5 and 5 mM DTT) + 1 uL reservoir (12% (w/v) polyethylene glycol 6000, 5% glycerol, 100 mM KCl, and 10 mM MgCl2 buffer), equilibrated against 1mL of reservoir in Nextal hanging drop plate format.	Resolution 2.45 Å R-free 0.213

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 6AZE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2RI7 Crystal structure of PHD finger-linker-bromodomain Y17E mutant from human BPTF in the H3(1-9)K4ME2 bound state Deposited 2007-10-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2726–2894（169 aa） Fragment：PHD-type 2 domain and Bromo domain; residues 2726-2894	Mutation：Y2737E	ZN ZINC ION × 2 GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；BPTF Y17E PHD finger-linker-bromodomain (16.5 mg/ml, 20 mM Tris-HCl pH 7.5, 50 mM KCl) was pre-incubated with three-fold molar excess of H3(1-9)K4me2 peptide in the presence of 5 mM MgCl2 for about 30 min on ice. Drops were made by mixing 2 l each of the complex with the reservoir solution: 8.5% isopropanol, 0.085 M Hepes-Na, pH 7.5, 17% PEG 4000, 15% Glycerol. A 0.3 l of 1 M KCl was then added to the drops as additive., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.45 Å R-free 0.192
3QZS Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form I Deposited 2011-03-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2924–3033（110 aa）	Mutation：K2998A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；100 mM Tris-HCl pH 8.0, 20% Glycerol, vapor diffusion, hanging drop	Resolution 1.80 Å R-free 0.230
3QZS Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form I Deposited 2011-03-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2924–3033（110 aa）	Mutation：K2998A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；100 mM Tris-HCl pH 8.0, 20% Glycerol, vapor diffusion, hanging drop	Resolution 1.80 Å R-free 0.230
3QZT Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form II Deposited 2011-03-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2924–3033（110 aa） Fragment：bromodomain (UNP residues 2924-3037)	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；20% (W/V) PEGMME 2K, 20% Glycerol and 0.2 M KCl, 0.1 M Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.198
3QZV Crystal Structure of BPTF PHD-linker-bromo in complex with histone H4K12ac peptide Deposited 2011-03-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2865–3033（169 aa） Fragment：BPTF (UNP Residues 2865-3033)	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% (W/V) PEG3000, 0.3 M NaAcetate, 0.1 M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.234
3UV2 Crystal structure of the bromodomain of human nucleosome-remodeling factor subunit BPTF Deposited 2011-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2914–3037（124 aa） Fragment：unp residues 2914-3037	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；293 K；0.10M Na/KPO4, 20.0% PEG 3350, 10.0% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.58 Å R-free 0.209
5H6Y The BPTF Bromodomain Recognising H4K12Cr peptide Deposited 2016-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2921–3036（116 aa） Fragment：UNP RESIDUES 2921-3036	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1 M succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1% PEG MME 2000	Resolution 2.00 Å R-free 0.224
5R4G PanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF in complex with FMOPL000621a Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 1 RU4 4-(1,2,3-thiadiazol-4-yl)phenyl ethylcarbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2	Resolution 1.25 Å R-free 0.208
5R4H PanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF in complex with FMOPL000287a Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 HWH ~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2	Resolution 1.18 Å R-free 0.205
5R4I PanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF in complex with FMOPL000443a Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 RUV 4-(acetylamino)-N-(4H-1,2,4-triazol-4-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2	Resolution 1.28 Å R-free 0.233
5R4J PanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF in complex with FMOPL000280a Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 RUY 4-(piperidin-1-yl)-1,2,5-oxadiazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2	Resolution 1.39 Å R-free 0.241
5R4K PanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF in complex with FMOPL000292a Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 K0V methyl 1-(tert-butylcarbamoyl)piperidine-4-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2	Resolution 1.17 Å R-free 0.225
5R4L PanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF in complex with FMOPL000349a Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 RV4 N-{4-[(morpholin-4-yl)methyl]phenyl}acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2	Resolution 1.13 Å R-free 0.209
5R4M PanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF in complex with FMOPL000513a Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 M25 N-{2-[4-(AMINOSULFONYL)PHENYL]ETHYL}ACETAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2	Resolution 1.11 Å R-free 0.221
5R4N PanDDA analysis group deposition -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF in complex with FMOPL000061a Deposited 2020-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 K3D 4-acetyl-N-ethylpiperazine-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2	Resolution 1.28 Å R-free 0.257
5R4O PanDDA analysis group deposition of ground-state model of BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF Deposited 2020-02-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris pH 8.5, 0.2M MgCl2	Resolution 1.05 Å R-free 0.178
7DMY The crystal structure of Cpd7 in complex with BPTF bromodomain Deposited 2020-12-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa） Fragment：Bromodomain	Not recorded	HAF tert-butyl 3-methyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]-4-oxidanylidene-5,7-dihydropyrrolo[3,4-d]pyrimidine-6-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Ammonium acetate, 20% PEG 3350, pH 7.1	Resolution 2.00 Å R-free 0.288
7DN4 The crystal structure of Cpd8 in complex with BPTF bromodomain Deposited 2020-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2917–3037（121 aa） Fragment：Bromodoamin and PHD finger Chain B 2917–3037（121 aa） Fragment：Bromodoamin and PHD finger Chain C 2917–3037（121 aa） Fragment：Bromodoamin and PHD finger Chain D 2917–3037（121 aa） Fragment：Bromodoamin and PHD finger Chain E 2917–3037（121 aa） Fragment：Bromodoamin and PHD finger Chain F 2917–3037（121 aa） Fragment：Bromodoamin and PHD finger	Not recorded	JC3 3-methyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-one × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；2 M Ammonium sulfate, 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate, pH5.6	Resolution 2.84 Å R-free 0.346
7JT4 Crystal Structure of BPTF bromodomain labelled with 5-fluoro-tryptophan Deposited 2020-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa） Fragment：bromodomain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% (w/v) polyethylene glycol 1500 and 10% (w/v) proprionate-cacodylate-bis tris propane	Resolution 2.06 Å R-free 0.186
7K6R Crystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to GSK4027 Deposited 2020-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	9ST 4-bromo-2-methyl-5-[[(3~{R},5~{R})-1-methyl-5-phenyl-piperidin-3-yl]amino]pyridazin-3-one × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Lithium sulfate monohydrate, 0.1M BIS-TRIS, 25 percent Polyethylene glycol 3,350	Resolution 1.60 Å R-free 0.197
7K6S Crystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to Compound 4 (SKT1174) Deposited 2020-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	VYM (7-amino-3,4-dihydroquinolin-1(2H)-yl)(cyclopropyl)methanone × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS, 25 percent Polyethylene glycol 3,350	Resolution 1.23 Å R-free 0.203
7KDW Crystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to Compound 6 (HZ01052) Deposited 2020-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	WCV cyclopropyl[7-({2-[(prop-2-yn-1-yl)amino]pyrimidin-4-yl}amino)-3,4-dihydroquinolin-1(2H)-yl]methanone × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH6.5, 25 percent polyethylene glycol 3,350	Resolution 1.71 Å R-free 0.246
7KDW Crystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to Compound 6 (HZ01052) Deposited 2020-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2917–3037（121 aa）	Not recorded	WCV cyclopropyl[7-({2-[(prop-2-yn-1-yl)amino]pyrimidin-4-yl}amino)-3,4-dihydroquinolin-1(2H)-yl]methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH6.5, 25 percent polyethylene glycol 3,350	Resolution 1.71 Å R-free 0.246
7KDZ Crystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to TP-238 Deposited 2020-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 WCS 6-{4-[3-(dimethylamino)propoxy]phenyl}-2-(methylsulfonyl)-N-[3-(1H-pyrazol-1-yl)propyl]pyrimidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH6.5, 25 percent polyethylene glycol 3,350	Resolution 1.54 Å R-free 0.205
7LP0 Crystal structure of BPTF bromodomain in complex with inhibitor Pdy-3-077 Deposited 2021-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	P2L 4-chlorol-2-methyl-5-[[(3~{R})-1-methylpiperidin-3-yl]amino]pyridazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% PEG 3,350	Resolution 1.66 Å R-free 0.235
7LP0 Crystal structure of BPTF bromodomain in complex with inhibitor Pdy-3-077 Deposited 2021-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	P2L 4-chlorol-2-methyl-5-[[(3~{R})-1-methylpiperidin-3-yl]amino]pyridazin-3-one × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% PEG 3,350	Resolution 1.66 Å R-free 0.235
7LPK Crystal structure of BPTF bromodomain in complex with inhibitor HZ-03-112 Deposited 2021-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	Y9P 4-chloranyl-2-methyl-5-[[(3~{R})-pyrrolidin-3-yl]amino]pyridazin-3-one × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% polyethylene glycol 3,350	Resolution 1.39 Å R-free 0.204
7LPK Crystal structure of BPTF bromodomain in complex with inhibitor HZ-03-112 Deposited 2021-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	Y9P 4-chloranyl-2-methyl-5-[[(3~{R})-pyrrolidin-3-yl]amino]pyridazin-3-one × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% polyethylene glycol 3,350	Resolution 1.39 Å R-free 0.204
7LRK Crystal structure of BPTF bromodomain in complex with inhibitor Pdy-3-093 Deposited 2021-02-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	YC4 4-chloranyl-2-methyl-5-[[(3~{S})-pyrrolidin-3-yl]amino]pyridazin-3-one × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% polyethylene glycol 3,350	Resolution 1.44 Å R-free 0.188
7LRK Crystal structure of BPTF bromodomain in complex with inhibitor Pdy-3-093 Deposited 2021-02-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	YC4 4-chloranyl-2-methyl-5-[[(3~{S})-pyrrolidin-3-yl]amino]pyridazin-3-one × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% polyethylene glycol 3,350	Resolution 1.44 Å R-free 0.188
7LRO Crystal structure of BPTF bromodomain in complex with inhibitor HZ-01-105 Deposited 2021-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	DMS DIMETHYL SULFOXIDE × 1 YBV 5-(azetidin-3-ylamino)-4-chloranyl-2-methyl-pyridazin-3-one × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% polyethylene glycol 3,350	Resolution 1.45 Å R-free 0.191
7LRO Crystal structure of BPTF bromodomain in complex with inhibitor HZ-01-105 Deposited 2021-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	YBV 5-(azetidin-3-ylamino)-4-chloranyl-2-methyl-pyridazin-3-one × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% polyethylene glycol 3,350	Resolution 1.45 Å R-free 0.191
7M2E Crystal structure of BPTF bromodomain in complex with CB02-092 Deposited 2021-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	YOV 4-chloro-5-{4-[2-(dimethylamino)ethyl]anilino}-2-methylpyridazin-3(2H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0. 2M NaCl and 23% PEG 3350	Resolution 1.75 Å R-free 0.215
7RWN Crystal Structure of BPTF bromodomain in complex with 4-chloro-5-{4-[(dimethylamino)methyl]anilino}-2-methylpyridazin-3(2H)-one Deposited 2021-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	7WE 4-chloro-5-{4-[(dimethylamino)methyl]anilino}-2-methylpyridazin-3(2H)-one × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；200 mM manganese acetate and 2% (v/v) PEG 3350	Resolution 1.39 Å R-free 0.179
7RWO Crystal Structure of BPTF bromodomain in complex with 4-chloro-2-methyl-5-[(1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyridazin-3(2H)-one Deposited 2021-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	7WN 4-chloro-2-methyl-5-[(1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyridazin-3(2H)-one × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；25% (w/v) polyethylene glycol 1500 and 10% (w/v) proprionate-cacodylate-bis tris propane	Resolution 1.58 Å R-free 0.207
7RWP Crystal Structure of BPTF bromodomain in complex with 5-[4-(aminomethyl)anilino]-4-chloro-2-methylpyridazin-3(2H)-one Deposited 2021-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	7WZ 5-[4-(aminomethyl)anilino]-4-chloro-2-methylpyridazin-3(2H)-one × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20% (v/v) PEG 3350	Resolution 1.73 Å R-free 0.207
7RWQ Crystal Structure of BPTF bromodomain in complex with 4-chloro-2-methyl-5-[(1,2,3,4-tetrahydroisoquinolin-6-yl)amino]pyridazin-3(2H)-one Deposited 2021-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	7XE 4-chloro-2-methyl-5-[(1,2,3,4-tetrahydroisoquinolin-6-yl)amino]pyridazin-3(2H)-one × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20% (v/v) PEG 3350	Resolution 1.90 Å R-free 0.219
8AG2 Crystal structure of the BPTF bromodomain in complex with BI-7190 Deposited 2022-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	M1I 5-[3-methoxy-4-[1-(4-methylpiperazin-1-yl)cyclopropyl]phenyl]-1,3,4-trimethyl-pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；32 % PEG1 000 200 mM magnesium chloride 100 mM sodium cacodylate	Resolution 1.02 Å R-free 0.171
8F6G Crystal structure of BPTF bromodomain in complex with BZ2 Deposited 2022-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa） Fragment：BPTF bromodomain (uniprot residues 2917-3037)	Not recorded	XHK 6-[4-(2-aminoethyl)anilino]-5-chloro-3-methylpyrimidin-4(3H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0. 2 M NaCl and 23% PEG 3350	Resolution 1.95 Å R-free 0.226
8OU2 Crystal structure of the bromodomain of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to a potent inhibitor Deposited 2023-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2917–3037（121 aa）	Not recorded	W2W 7-(1-cyclopropylpyrazol-4-yl)-2-[[2-fluoranyl-4-(4-methylpiperazin-1-yl)sulfonyl-phenyl]amino]-3-methyl-pyrido[1,2-a]pyrimidin-4-one × 1 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.20M KSCN; 0.1M BTProp pH 6.5; 20.0% PEG 3350; 10.0% EtGly	Resolution 1.60 Å R-free 0.222
8OU2 Crystal structure of the bromodomain of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to a potent inhibitor Deposited 2023-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2917–3037（121 aa）	Not recorded	W2W 7-(1-cyclopropylpyrazol-4-yl)-2-[[2-fluoranyl-4-(4-methylpiperazin-1-yl)sulfonyl-phenyl]amino]-3-methyl-pyrido[1,2-a]pyrimidin-4-one × 1 EDO 1,2-ETHANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.20M KSCN; 0.1M BTProp pH 6.5; 20.0% PEG 3350; 10.0% EtGly	Resolution 1.60 Å R-free 0.222

34 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BPTF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 2866–3032

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6aze
Deposition date deposition_date	2017-09-11
Structure title title	Crystal Structure of the BPTF PHD-bromodomain module bound to H3KC4me3 methyl lysine analog
Keywords keywords	PHD-finger, bromodomain, histone reader, methyllsine analog, MLA, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.54 Å
Radius of gyration Rg (electron density) rg_electron	23.20 Å
Forward intensity I(0) i0	7484320.00
Molecular weight molecular_weight	20296.0 kDa
Excluded volume excluded_volume	25242 Å³
Envelope volume envelope_volume	32106 Å³
Hydration-shell volume shell_volume	13104 Å³
Envelope diameter envelope_diameter	83.6 Å
Shell Rg shell_rg	27.38 Å
Envelope Rg envelope_rg	23.22 Å
Shape Rg shape_rg	23.22 Å
Total Rg total_rg	23.74 Å
Total atoms total_atoms	1415
Residues n_residues	172
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	82.7 Å
Rg (real space) rg_real	23.86 Å
Rg uncertainty (real space) rg_real_error	1.09 Å
I(0) (real space) i0_real	7.4840e+06
I(0) uncertainty (real space) i0_real_error	1.2560e+05
Rg (reciprocal space) rg_reciprocal	23.79 Å
I(0) (reciprocal space) i0_reciprocal	7484000.0000
Solution quality estimate total_estimate	0.7284
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.1 Å
Skewness Skewness skewness	0.471
Kurtosis Kurtosis kurtosis	-0.628
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	907600.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.434; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.218; Smooth: 0.963

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nucleosome-remodeling factor subunit BPTF
Molecular weight formula_weight	19699.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1517

TKLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK

来源 Source

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

Entity 2 Entity 2 polymer

Description description	ALA-ARG-THR-ML3-GLN-THR
Molecular weight formula_weight	765.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ARTKQT

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6azeA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6azeA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

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8. Citations (1)

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Unit-cell length a length_a	38.263 Å
Unit-cell length b length_b	64.130 Å
Unit-cell length c length_c	85.670 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.451 Å
Low-resolution limit resolution_low	23.623 Å
R factor r_factor	0.1814
R_work r_work	0.1797
R_free r_free	0.2131

fit	/app/data/saxs_computation/az/6aze/6aze.fit
pddf	/app/data/pr_computation/az/6aze/6aze.pr.out
profile	/app/data/saxs_computation/az/6aze/6aze.dat

Crystal Structure of the BPTF PHD-bromodomain module bound to H3KC4me3 methyl lysine analog

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

Nucleosome-remodeling factor subunit BPTF

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)