SAXSdb — 5dkd

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

Transcription activator BRG1

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 1418–1536	Fragment：UNP residues 1418-1536	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 5BW (2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；277.15 K；0.1 M Bis Tris pH 7.2, 0.1 M ammonium acetate, 0.1 M ZnCl2, 15% PEG smear high (mixture from PEG8k to 20k)	Resolution 2.00 Å R-free 0.297
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1418–1536	Fragment：UNP residues 1418-1536	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 5BW (2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；277.15 K；0.1 M Bis Tris pH 7.2, 0.1 M ammonium acetate, 0.1 M ZnCl2, 15% PEG smear high (mixture from PEG8k to 20k)	Resolution 2.00 Å R-free 0.297

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 5DKD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GRC 1.5 A structure of bromodomain from human BRG1 protein, a central ATPase of SWI/SNF remodeling complex Deposited 2006-04-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1448–1575（128 aa） Fragment：bromodomain, residues 1448-1575	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1 M Tris, 25% w/v PEG 3350, pH 8.5, VAPOR DIFFUSION, temperature 298.0K	Resolution 1.50 Å R-free 0.264
2H60 Solution Structure of Human Brg1 Bromodomain Deposited 2006-05-30	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 1452–1570（119 aa） Fragment：Bromodomain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；293 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR sample composition 1mM Brg1 bromodomain U-15N, 13C; 25mM phosphate buffer; 100mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3UVD Crystal Structure of the bromodomain of human Transcription activator BRG1 (SMARCA4) in complex with N-Methyl-2-pyrrolidone Deposited 2011-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1448–1569（122 aa） Fragment：unp residues 1448-1569	Not recorded	MB3 1-methylpyrrolidin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；28% MMW PEG smear 0.1M Tris.HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.85 Å R-free 0.262
5EA1 Crystal Structure of SMARCA4 bromodomain in complex with MPD Deposited 2015-10-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1451–1580（130 aa） Fragment：Bromodomain, UNP residues 1451-1580	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG1000 (12.5%), PEG3350 (12.5%), MPD (12.5%)	Resolution 2.00 Å R-free 0.228
5EA1 Crystal Structure of SMARCA4 bromodomain in complex with MPD Deposited 2015-10-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1451–1580（130 aa） Fragment：Bromodomain, UNP residues 1451-1580	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG1000 (12.5%), PEG3350 (12.5%), MPD (12.5%)	Resolution 2.00 Å R-free 0.228
5EA1 Crystal Structure of SMARCA4 bromodomain in complex with MPD Deposited 2015-10-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1451–1580（130 aa） Fragment：Bromodomain, UNP residues 1451-1580	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG1000 (12.5%), PEG3350 (12.5%), MPD (12.5%)	Resolution 2.00 Å R-free 0.228
6HR2 Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB Deposited 2018-09-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1416–1535（120 aa）	Not recorded	FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% (w/v) PEG1500, 0.1 M MIB Buffer, pH 6.0	Resolution 1.76 Å R-free 0.236
6HR2 Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB Deposited 2018-09-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1416–1535（120 aa）	Not recorded	FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% (w/v) PEG1500, 0.1 M MIB Buffer, pH 6.0	Resolution 1.76 Å R-free 0.236
6LTH Structure of human BAF Base module Deposited 2020-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain I 1–1647（1647 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6LTJ Structure of nucleosome-bound human BAF complex Deposited 2020-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain I 1–1647（1647 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6ZS2 Crystal Structure of the bromodomain of human transcription activator BRG1 (SMARCA4) in complex with 2-(6-amino-5-(piperazin-1-yl)pyridazin-3-yl)phenol Deposited 2020-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1418–1536（119 aa）	Not recorded	FX5 2-(6-azanyl-5-piperazin-4-ium-1-yl-pyridazin-3-yl)phenol × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Crystallization buffer: 20% medium-molecular-weight PEG smear, 0.1 M Tris pH 8.5	Resolution 1.57 Å R-free 0.215
6ZS2 Crystal Structure of the bromodomain of human transcription activator BRG1 (SMARCA4) in complex with 2-(6-amino-5-(piperazin-1-yl)pyridazin-3-yl)phenol Deposited 2020-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1418–1536（119 aa）	Not recorded	FX5 2-(6-azanyl-5-piperazin-4-ium-1-yl-pyridazin-3-yl)phenol × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Crystallization buffer: 20% medium-molecular-weight PEG smear, 0.1 M Tris pH 8.5	Resolution 1.57 Å R-free 0.215
7VDT The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex 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–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain A 160–1614（1455 aa）	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7VDV The overall structure of human chromatin remodeling PBAF-nucleosome complex 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–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain A 160–1614（1455 aa）	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7Y8R The nucleosome-bound human PBAF complex Deposited 2022-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric	Chain I 1–1647（1647 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
8EB1 Chim2 - Intragenic antimicrobial peptide Deposited 2022-08-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 874–878（5 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) PBS 10 mM；Pressure 1 NMR sample composition 1.28 mM peptide, 32 mM D-98% Dodecylphosphorylcholine-d38, 10 mM PBS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8G1Q Co-crystal structure of Compound 1 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB Deposited 2023-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1447–1569（123 aa）	Not recorded	NA SODIUM ION × 1 YHB N-(2-{4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}pyridine-4-carbonyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；PEG 300 0.1M Bis-Tris 6.5	Resolution 3.73 Å R-free 0.326
8QJR BRG1 bromodomain in complex with VBC via compound 17 Deposited 2023-09-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1418–1536（119 aa） Fragment：UNP residues 1418-1536	Not recorded	PO4 PHOSPHATE ION × 5 GOL GLYCEROL × 1 VLH (2S,4R)-1-[(2R)-2-[3-[2-[4-[3-[4-[(1R,5S)-3-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]pyridin-2-yl]oxycyclobutyl]oxypiperidin-1-yl]ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；27 mM HEPES pH 6.8, 73 mM HEPES pH 8.6, 1.0 M NaI	Resolution 3.17 Å R-free 0.278
8QJR BRG1 bromodomain in complex with VBC via compound 17 Deposited 2023-09-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1418–1536（119 aa） Fragment：UNP residues 1418-1536	Not recorded	PO4 PHOSPHATE ION × 2 VLH (2S,4R)-1-[(2R)-2-[3-[2-[4-[3-[4-[(1R,5S)-3-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]pyridin-2-yl]oxycyclobutyl]oxypiperidin-1-yl]ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；27 mM HEPES pH 6.8, 73 mM HEPES pH 8.6, 1.0 M NaI	Resolution 3.17 Å R-free 0.278
9DTX Crystal structure of PRT3789 in complex with the bromodomain of human BRG1 (SMARCA4) and pVHL:ElonginC:ElonginB Deposited 2024-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1448–1569（122 aa） Fragment：UNP residues 1448-1569	Not recorded	A1BB4 (4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M Bis-Tris propane, pH 8.5, 0.2 M potassium thiocyanate, 20% w/v PEG3350	Resolution 2.11 Å R-free 0.232
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric	Chain I 1–1647（1647 aa）	Not recorded	PTD PENTANEDIAL × 16 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric	Chain I 1–1647（1647 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric	Chain I 1–1647（1647 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric	Chain I 1–1647（1647 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9UX9 local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state Deposited 2025-05-13	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: 11-meric	Chain K 2–1647（1646 aa）	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9UXA local ARP-NCP structure of the ncBAF-nucleosome complex in the apo state Deposited 2025-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain K 2–1647（1646 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
9UXB The apo structure of BCL7B-containing ARP module of the human SWI/SNF complex Deposited 2025-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 446–517（72 aa）	Not recorded	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å
9UXC The ADP-bound structure of BCL7B-containing ARP module of the human SWI/SNF complex Deposited 2025-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 446–517（72 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.74 Å
9WBZ The structure of NCP-motor-ARP module of ncBAF-nucleosome complex Deposited 2025-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain A 1–1614（1614 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9WC1 The structure of ARP module in ncBAF complex Deposited 2025-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–1614（1614 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

25 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SMCA4_HUMAN
Isoform	P51532-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–121； UniProt 1418–1536 Author chain B； PDBConstruct 3–121； UniProt 1418–1536

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5dkd
Deposition date deposition_date	2015-09-03
Structure title title	Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe
Keywords keywords	SWI-SNF complex, chromatin remodeling, Brg associated factors (BAF), transcription, hydrolase; HYDROLASE
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	21.00 Å
Radius of gyration Rg (electron density) rg_electron	20.07 Å
Forward intensity I(0) i0	12195600.00
Molecular weight molecular_weight	27129.0 kDa
Excluded volume excluded_volume	34502 Å³
Envelope volume envelope_volume	42541 Å³
Hydration-shell volume shell_volume	18097 Å³
Envelope diameter envelope_diameter	71.7 Å
Shell Rg shell_rg	25.97 Å
Envelope Rg envelope_rg	20.06 Å
Shape Rg shape_rg	20.07 Å
Total Rg total_rg	21.00 Å
Total atoms total_atoms	1901
Residues n_residues	220
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	68.1 Å
Rg (real space) rg_real	20.96 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.2200e+07
I(0) uncertainty (real space) i0_real_error	1.5830e+05
Rg (reciprocal space) rg_reciprocal	20.97 Å
I(0) (reciprocal space) i0_reciprocal	12200000.0000
Solution quality estimate total_estimate	0.8208
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.238
Kurtosis Kurtosis kurtosis	-0.485
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2453000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Transcription activator BRG1
Molecular weight formula_weight	14230.4 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2002

SMLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDD

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 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	(2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-one
Molecular weight formula_weight	321.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	101

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5dkda_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.0 — automated matches

Domain ID domain_id	d5dkdb_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5dkdA00
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

Domain ID domain_id	5dkdB00
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	45.926 Å
Unit-cell length b length_b	74.566 Å
Unit-cell length c length_c	52.626 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.780 Å
R factor r_factor	0.2692
R_work r_work	0.2677
R_free r_free	0.2973

fit	/app/data/saxs_computation/dk/5dkd/5dkd.fit
pddf	/app/data/pr_computation/dk/5dkd/5dkd.pr.out
profile	/app/data/saxs_computation/dk/5dkd/5dkd.dat

Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe

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

Transcription activator BRG1

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