1wum

Complex structure of PCAF bromodomain with small chemical ligand NP2

Method: SOLUTION NMR D_max: 58.0 Å Quality: GOOD

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

Histone acetyltransferase PCAF

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 719–832	Fragment：BROMODOMAIN	NP2 N-(3-AMINOPROPYL)-2-NITROBENZENAMINE × 1	SOLUTION NMR NMR measurement conditions：pH 6.5；303 K NMR sample composition：0.5mM sample in 100mM phosphate buffer containing 5mM perdeuterated DTT \| 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 1WUM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CM0 CRYSTAL STRUCTURE OF THE PCAF/COENZYME-A COMPLEX Deposited 1999-05-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 491–658（168 aa） Fragment：HISTONE ACETYLTRANSFERASE DOMAIN	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；5MG/ML OF P/CAF WITH 2 M EXCESS COFACTOR, 100MM TRIS, 1.5 M LITHIUM SULFATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.268
1CM0 CRYSTAL STRUCTURE OF THE PCAF/COENZYME-A COMPLEX Deposited 1999-05-12	Different construct 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 491–658（168 aa） Fragment：HISTONE ACETYLTRANSFERASE DOMAIN	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；5MG/ML OF P/CAF WITH 2 M EXCESS COFACTOR, 100MM TRIS, 1.5 M LITHIUM SULFATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.268
1JM4 NMR Structure of P/CAF Bromodomain in Complex with HIV-1 Tat Peptide Deposited 2001-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 448–561（114 aa） Fragment：Bromodomain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 100 mM；Pressure Ambient NMR sample composition 0.5 mM Bromodomain (U-15N)/Tat Peptide; 100 mM Phosphate Buffer of pH 6.5, 5 mM Perdeuterated DTT and 0.5 mM EDTA \| 90% H2O/10% D2O NMR sample composition 0.5 mM Bromodomain (U-13C,15N)/Tat Peptide; 100 mM Phosphate Buffer of pH 6.5, 5 mM Perdeuterated DTT and 0.5 mM EDTA \| 99.5% D2O NMR sample composition 0.5 mM Bromodomain (U-13C,15N, 75%-2H)/Tat Peptide; 100 mM Phosphate Buffer of pH 6.5, 5 mM Perdeuterated DTT and 0.5 mM EDTA \| 90% H2O/10% D2O	Resolution not provided
1N72 Structure and Ligand of a Histone Acetyltransferase Bromodomain Deposited 2002-11-12	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 719–832（114 aa） Fragment：Bromodomain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 200；Pressure 1 NMR sample composition 1mM Bromodomain, 100mM Sodium phosphate, 5mM DTT-d10, 0.5mM EDTA, pH 6.5 \| 90% H2O/10% D2O	Resolution not provided
1WUG complex structure of PCAF bromodomain with small chemical ligand NP1 Deposited 2004-12-07	Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 719–832（114 aa） Fragment：BROMODOMAIN	Not recorded	NP1 N-(3-AMINOPROPYL)-4-METHYL-2-NITROBENZENAMINE × 1	SOLUTION NMR NMR measurement conditions pH 6.5；303 K NMR sample composition 0.5mM sample in 100mM phosphate buffer containing 5mM perdeuterated DTT \| 10% D2O	Resolution not provided
1ZS5 Structure-based evaluation of selective and non-selective small molecules that block HIV-1 TAT and PCAF association Deposited 2005-05-23	Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 719–832（114 aa） Fragment：BROMODOMAIN	Not recorded	MIB (3E)-4-(1-METHYL-1H-INDOL-3-YL)BUT-3-EN-2-ONE × 1	SOLUTION NMR NMR measurement conditions pH 6.5；303 K NMR sample composition 0.5mM sample in 100mM phosphate buffer containing 5mM perdeuterated DTT, 10% D2O \| 10% D2O NMR sample composition 0.5mM sample in 100mM phosphate buffer containing 5mM perdeuterated DTT, 100% D2O \| 100% D2O	Resolution not provided
2RNW The Structural Basis for Site-Specific Lysine-Acetylated Histone Recognition by the Bromodomains of the Human Transcriptional Co-Activators PCAf and CBP Deposited 2008-02-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 719–832（114 aa） Fragment：UNP residues 719-832	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] potassium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RNX The Structural Basis for Site-Specific Lysine-Acetylated Histone Recognition by the Bromodomains of the HUman Transcriptional Co-Activators PCAF and CBP Deposited 2008-02-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 719–832（114 aa） Fragment：UNP residues 719-832	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] potassium phosphate, 100% D2O \| 100% D2O	Resolution not provided
3GG3 Crystal Structure of the Bromodomain of Human PCAF Deposited 2009-02-27	Different construct 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 715–831（117 aa） Fragment：UNP residues 715-831	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；20% PEG10K, 4% Ethylene Glycol, 0.1M HEPES pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.25 Å R-free 0.245
3GG3 Crystal Structure of the Bromodomain of Human PCAF Deposited 2009-02-27	Different construct 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 715–831（117 aa） Fragment：UNP residues 715-831	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；20% PEG10K, 4% Ethylene Glycol, 0.1M HEPES pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.25 Å R-free 0.245
4NSQ Crystal structure of PCAF Deposited 2013-11-28	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 493–658（166 aa） Fragment：UNP Residues 493-658 Chain D 493–658（166 aa） Fragment：UNP Residues 493-658	Not recorded	COA COENZYME A × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；298 K；0.2M Lithium Sulfate, 0.1M HEPES pH7.4, 1.2M Ammonium Sulfate and 10mM Trimethylamine HCl, VAPOR DIFFUSION, temperature 298K	Resolution 2.31 Å R-free 0.275
4NSQ Crystal structure of PCAF Deposited 2013-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 493–658（166 aa） Fragment：UNP Residues 493-658 Chain C 493–658（166 aa） Fragment：UNP Residues 493-658	Not recorded	COA COENZYME A × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；298 K；0.2M Lithium Sulfate, 0.1M HEPES pH7.4, 1.2M Ammonium Sulfate and 10mM Trimethylamine HCl, VAPOR DIFFUSION, temperature 298K	Resolution 2.31 Å R-free 0.275
5FDZ Crystal structure of human PCAF bromodomain in complex with compound BDOMB00091a (compound 14) Deposited 2015-12-16	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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831 Chain B 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	5X0 ~{N}-methyl-2-(oxan-4-yloxy)-5-(2-oxidanylidene-2-phenylazanyl-ethoxy)benzamide × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.40 Å R-free 0.244
5FE0 Crystal structure of human PCAF bromodomain in complex with acetyllysine Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP residues 715-831	Not recorded	ALY N(6)-ACETYLLYSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.30 Å R-free 0.246
5FE0 Crystal structure of human PCAF bromodomain in complex with acetyllysine Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP residues 715-831	Not recorded	ALY N(6)-ACETYLLYSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.30 Å R-free 0.246
5FE1 Crystal structure of human PCAF bromodomain in complex with fragment BR004 (fragment 1) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP residues 715-831	Not recorded	12Q 1-METHYLQUINOLIN-2(1H)-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.22 Å R-free 0.241
5FE1 Crystal structure of human PCAF bromodomain in complex with fragment BR004 (fragment 1) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP residues 715-831	Not recorded	12Q 1-METHYLQUINOLIN-2(1H)-ONE × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.22 Å R-free 0.241
5FE2 Crystal structure of human PCAF bromodomain in complex with fragment BR013 (fragment 3) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	5WV 2-methyl-3~{H}-isoindol-1-one × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.25 Å R-free 0.237
5FE2 Crystal structure of human PCAF bromodomain in complex with fragment BR013 (fragment 3) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	5WV 2-methyl-3~{H}-isoindol-1-one × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.25 Å R-free 0.237
5FE3 Crystal structure of human PCAF bromodomain in complex with fragment MB360 (fragment 4) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 3 5WX 4-methoxy-1,2-benzoxazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.12 Å R-free 0.237
5FE3 Crystal structure of human PCAF bromodomain in complex with fragment MB360 (fragment 4) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 3 5WX 4-methoxy-1,2-benzoxazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.12 Å R-free 0.237
5FE4 Crystal structure of human PCAF bromodomain in complex with fragment MB364 (fragment 5) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 2 5WY 2,3-dihydro-1,4-benzodioxine-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.15 Å R-free 0.232
5FE4 Crystal structure of human PCAF bromodomain in complex with fragment MB364 (fragment 5) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 3 5WY 2,3-dihydro-1,4-benzodioxine-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.15 Å R-free 0.232
5FE5 Crystal structure of human PCAF bromodomain in complex with fragment MB093 (fragment 7) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.12 Å R-free 0.251
5FE5 Crystal structure of human PCAF bromodomain in complex with fragment MB093 (fragment 7) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 5 2QC 1-[4-(1,2,3-thiadiazol-4-yl)phenyl]methanamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.12 Å R-free 0.251
5FE6 Crystal structure of human PCAF bromodomain in complex with fragment ZB1916 (fragment 10) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 8 5WZ (4-azanylpiperidin-1-yl)-cyclopropyl-methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 1.77 Å R-free 0.212
5FE6 Crystal structure of human PCAF bromodomain in complex with fragment ZB1916 (fragment 10) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP Residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 1.77 Å R-free 0.212
5FE7 Crystal structure of human PCAF bromodomain in complex with fragment ZB2216 (fragment 11) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 1 5WU 1-(2-hydroxyethyl)-3-methyl-6,7-dihydro-5~{H}-indazol-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.08 Å R-free 0.213
5FE7 Crystal structure of human PCAF bromodomain in complex with fragment ZB2216 (fragment 11) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.08 Å R-free 0.213
5FE8 Crystal structure of human PCAF bromodomain in complex with compound SL1126 (compound 12) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP residues 715-831	Not recorded	5WT ~{N}-(1,4-dimethyl-2-oxidanylidene-quinolin-7-yl)ethanamide × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.10 Å R-free 0.233
5FE8 Crystal structure of human PCAF bromodomain in complex with compound SL1126 (compound 12) Deposited 2015-12-16	Different construct 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 715–831（117 aa） Fragment：PCAF bromodomain, UNP residues 715-831	Not recorded	EDO 1,2-ETHANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.10 Å R-free 0.233
5FE9 Crystal structure of human PCAF bromodomain in complex with compound SL1122 (compound 13) Deposited 2015-12-16	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 715–831（117 aa） Fragment：UNP residues 715-831 Chain B 715–831（117 aa） Fragment：UNP residues 715-831	Not recorded	5WS ~{N}-(1,4-dimethyl-2-oxidanylidene-quinolin-7-yl)methanesulfonamide × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.35 Å R-free 0.258
5LVQ Crystal structure of human PCAF bromodomain in complex with compound-D (CPD-D), N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide Deposited 2016-09-14	Different construct 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 715–831（117 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 2LX N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.05 Å R-free 0.218
5LVQ Crystal structure of human PCAF bromodomain in complex with compound-D (CPD-D), N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide Deposited 2016-09-14	Different construct 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 715–831（117 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.05 Å R-free 0.218
5LVR Crystal structure of human PCAF bromodomain in complex with compound-E (CPD-E) Deposited 2016-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 715–831（117 aa） Chain B 715–831（117 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6 78Y 5-methyl-2-phenyl-1,2,3-triazole-4-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8	Resolution 2.05 Å R-free 0.204
5MKX 1.68A STRUCTURE PCAF BROMODOMAIN WITH 4-chloro-2-methyl-5-(methylamino)pyridazin-3(2H)-one Deposited 2016-12-05	Different construct 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 715–831（117 aa）	Not recorded	82I 4-chloranyl-2-methyl-5-(methylamino)pyridazin-3-one × 1 SO4 SULFATE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；Morpheus condition 37	Resolution 1.68 Å R-free 0.206
5MKX 1.68A STRUCTURE PCAF BROMODOMAIN WITH 4-chloro-2-methyl-5-(methylamino)pyridazin-3(2H)-one Deposited 2016-12-05	Different construct 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 715–831（117 aa）	Not recorded	82I 4-chloranyl-2-methyl-5-(methylamino)pyridazin-3-one × 1 BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；Morpheus condition 37	Resolution 1.68 Å R-free 0.206
6J3O Crystal structure of the human PCAF bromodomain in complex with compound 12 Deposited 2019-01-05	Different construct 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 715–831（117 aa）	Not recorded	B4L 3-methyl-2-[[(3~{R})-1-methylpiperidin-3-yl]amino]-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM HEPES pH 8.2, 26% PEG10000 (v/v), 4% glycol	Resolution 2.11 Å R-free 0.257
6J3O Crystal structure of the human PCAF bromodomain in complex with compound 12 Deposited 2019-01-05	Different construct 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 715–831（117 aa）	Not recorded	B4L 3-methyl-2-[[(3~{R})-1-methylpiperidin-3-yl]amino]-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM HEPES pH 8.2, 26% PEG10000 (v/v), 4% glycol	Resolution 2.11 Å R-free 0.257

24 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PCAF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–118； UniProt 719–832

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	1wum
Deposition date deposition_date	2004-12-08
Structure title title	Complex structure of PCAF bromodomain with small chemical ligand NP2
Keywords keywords	BROMODOMAIN, HISTONE-ACETYLTRANSFERASE, NMR-STRUCTURE, CHEMICAL LIGAND, NP2, NP1, TRANSFERASE; TRANSFERASE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.12 Å
Radius of gyration Rg (electron density) rg_electron	14.79 Å
Forward intensity I(0) i0	3811780.00
Molecular weight molecular_weight	14197.0 kDa
Excluded volume excluded_volume	17949 Å³
Envelope volume envelope_volume	20469 Å³
Hydration-shell volume shell_volume	12062 Å³
Envelope diameter envelope_diameter	55.6 Å
Shell Rg shell_rg	20.16 Å
Envelope Rg envelope_rg	15.39 Å
Shape Rg shape_rg	14.78 Å
Total Rg total_rg	15.95 Å
Total atoms total_atoms	1999
Residues n_residues	118
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	58.0 Å
Rg (real space) rg_real	16.13 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	3.8120e+06
I(0) uncertainty (real space) i0_real_error	4.8500e+04
Rg (reciprocal space) rg_reciprocal	16.13 Å
I(0) (reciprocal space) i0_reciprocal	3812000.0000
Solution quality estimate total_estimate	0.8330
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.421
Kurtosis Kurtosis kurtosis	-0.062
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1024000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.646; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.891; Smooth: 0.996

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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1wuma2
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

Domain ID domain_id	d1wuma3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1wumA00
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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Description description	Histone acetyltransferase PCAF
Molecular weight formula_weight	14052.2 kDa
EC 编号 ec_number	2.3.1.48
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1999

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 BL21(DE3)

Description description	N-(3-AMINOPROPYL)-2-NITROBENZENAMINE
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/wu/1wum/1wum.fit
pddf	/app/data/pr_computation/wu/1wum/1wum.pr.out
profile	/app/data/saxs_computation/wu/1wum/1wum.dat

Complex structure of PCAF bromodomain with small chemical ligand NP2

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

Histone acetyltransferase PCAF

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)