8dkb

Crystal Structure of human YEATS4 in complex with Pfizer small molecule compound 3b

Method: X-RAY DIFFRACTION D_max: 120.2 Å Quality: EXCELLENT

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

YEATS domain-containing protein 4

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 1–149	Not recorded	SJI N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate (pH 5.6), 2% (v/v) tacsimate (pH 5.0), and 16% PEG 3350, 0.1M Ammonium sulfate	Resolution 2.58 Å R-free 0.226
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–149	Not recorded	SJI N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate (pH 5.6), 2% (v/v) tacsimate (pH 5.0), and 16% PEG 3350, 0.1M Ammonium sulfate	Resolution 2.58 Å R-free 0.226
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–149	Not recorded	SJI N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate (pH 5.6), 2% (v/v) tacsimate (pH 5.0), and 16% PEG 3350, 0.1M Ammonium sulfate	Resolution 2.58 Å R-free 0.226
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–149	Not recorded	SJI N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate (pH 5.6), 2% (v/v) tacsimate (pH 5.0), and 16% PEG 3350, 0.1M Ammonium sulfate	Resolution 2.58 Å R-free 0.226
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–149	Not recorded	SJI N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate (pH 5.6), 2% (v/v) tacsimate (pH 5.0), and 16% PEG 3350, 0.1M Ammonium sulfate	Resolution 2.58 Å R-free 0.226
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–149	Not recorded	SJI N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate (pH 5.6), 2% (v/v) tacsimate (pH 5.0), and 16% PEG 3350, 0.1M Ammonium sulfate	Resolution 2.58 Å R-free 0.226
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 1–149	Not recorded	SJI N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate (pH 5.6), 2% (v/v) tacsimate (pH 5.0), and 16% PEG 3350, 0.1M Ammonium sulfate	Resolution 2.58 Å R-free 0.226
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 1–149	Not recorded	SJI N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate (pH 5.6), 2% (v/v) tacsimate (pH 5.0), and 16% PEG 3350, 0.1M Ammonium sulfate	Resolution 2.58 Å R-free 0.226

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 8DKB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5R68 XChem group deposition -- Crystal Structure of human YEATS4 in complex with FM000199e Deposited 2020-02-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–190（173 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 RYD (1-methylbenzotriazol-5-yl)methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M tris pH 7.5, 0.15M lithium sulfate, 40% PEG400	Resolution 1.64 Å R-free 0.251
5R68 XChem group deposition -- Crystal Structure of human YEATS4 in complex with FM000199e Deposited 2020-02-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–190（173 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 RYD (1-methylbenzotriazol-5-yl)methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M tris pH 7.5, 0.15M lithium sulfate, 40% PEG400	Resolution 1.64 Å R-free 0.251
5R69 XChem group deposition -- Crystal Structure of human YEATS4 in complex with XS038644e Deposited 2020-02-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–190（173 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 ZHA ~{N}-(5-oxidanylidene-7,8-dihydro-6~{H}-naphthalen-2-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M tris pH 7.5, 0.15M lithium sulfate, 40% PEG400	Resolution 1.83 Å R-free 0.248
5R69 XChem group deposition -- Crystal Structure of human YEATS4 in complex with XS038644e Deposited 2020-02-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–190（173 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 ZHA ~{N}-(5-oxidanylidene-7,8-dihydro-6~{H}-naphthalen-2-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M tris pH 7.5, 0.15M lithium sulfate, 40% PEG400	Resolution 1.83 Å R-free 0.248
5VNA Crystal structure of human YEATS domain Deposited 2017-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa） Fragment：UNP residues 1-148	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.4；290 K；1.24 M ammonium sulfate, 100 mM CHES pH 9.4	Resolution 2.10 Å R-free 0.222
5VNA Crystal structure of human YEATS domain Deposited 2017-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–148（148 aa） Fragment：UNP residues 1-148	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.4；290 K；1.24 M ammonium sulfate, 100 mM CHES pH 9.4	Resolution 2.10 Å R-free 0.222
5VNA Crystal structure of human YEATS domain Deposited 2017-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–148（148 aa） Fragment：UNP residues 1-148	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.4；290 K；1.24 M ammonium sulfate, 100 mM CHES pH 9.4	Resolution 2.10 Å R-free 0.222
5VNA Crystal structure of human YEATS domain Deposited 2017-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–148（148 aa） Fragment：UNP residues 1-148	Not recorded	SO4 SULFATE ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.4；290 K；1.24 M ammonium sulfate, 100 mM CHES pH 9.4	Resolution 2.10 Å R-free 0.222
5VNB YEATS in complex with histone H3 Deposited 2017-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa） Fragment：UNP residues 1-148	Not recorded	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.4；290 K；1.36 M ammonium sulfate, 100 mM CHES pH 9.4	Resolution 2.40 Å R-free 0.248
5VNB YEATS in complex with histone H3 Deposited 2017-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–148（148 aa） Fragment：UNP residues 1-148	Not recorded	EDO 1,2-ETHANEDIOL × 6 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.4；290 K；1.36 M ammonium sulfate, 100 mM CHES pH 9.4	Resolution 2.40 Å R-free 0.248
5VNB YEATS in complex with histone H3 Deposited 2017-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–148（148 aa） Fragment：UNP residues 1-148	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.4；290 K；1.36 M ammonium sulfate, 100 mM CHES pH 9.4	Resolution 2.40 Å R-free 0.248
5VNB YEATS in complex with histone H3 Deposited 2017-04-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–148（148 aa） Fragment：UNP residues 1-148	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.4；290 K；1.36 M ammonium sulfate, 100 mM CHES pH 9.4	Resolution 2.40 Å R-free 0.248
5XTZ Crystal structure of GAS41 YEATS bound to H3K27ac peptide Deposited 2017-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 15–159（145 aa） Fragment：UNP RESIDUES 15-159 Chain B 15–159（145 aa） Fragment：UNP RESIDUES 15-159 Chain C 15–159（145 aa） Fragment：UNP RESIDUES 15-159 Chain D 15–159（145 aa） Fragment：UNP RESIDUES 15-159	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；0.1 M sodium acetate trihydrate, pH 4.6, 4.0 M ammonium acetate	Resolution 2.10 Å R-free 0.233
5XTZ Crystal structure of GAS41 YEATS bound to H3K27ac peptide Deposited 2017-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 15–159（145 aa） Fragment：UNP RESIDUES 15-159 Chain B 15–159（145 aa） Fragment：UNP RESIDUES 15-159 Chain C 15–159（145 aa） Fragment：UNP RESIDUES 15-159 Chain D 15–159（145 aa） Fragment：UNP RESIDUES 15-159	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；0.1 M sodium acetate trihydrate, pH 4.6, 4.0 M ammonium acetate	Resolution 2.10 Å R-free 0.233
5Y8V Crystal structure of GAS41 Deposited 2017-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–160（140 aa） Fragment：UNP residues 21-160	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；291 K；0.1M MES pH 6.5, 1.6M MgSO4	Resolution 2.61 Å R-free 0.280
5Y8V Crystal structure of GAS41 Deposited 2017-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–160（140 aa） Fragment：UNP residues 21-160	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；291 K；0.1M MES pH 6.5, 1.6M MgSO4	Resolution 2.61 Å R-free 0.280
5Y8V Crystal structure of GAS41 Deposited 2017-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 21–160（140 aa） Fragment：UNP residues 21-160	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；291 K；0.1M MES pH 6.5, 1.6M MgSO4	Resolution 2.61 Å R-free 0.280
5Y8V Crystal structure of GAS41 Deposited 2017-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 21–160（140 aa） Fragment：UNP residues 21-160	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；291 K；0.1M MES pH 6.5, 1.6M MgSO4	Resolution 2.61 Å R-free 0.280
7EIF Crystal structure of GAS41 YEATS domain Deposited 2021-03-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–159（141 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Bis-Tris buffer (pH 5.9) containing 3.3 M NaCl	Resolution 1.58 Å R-free 0.158
7JFY GAS41 YEATS domain in complex with 5 Deposited 2020-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–148（148 aa） Chain B 1–148（148 aa） Chain C 1–148（148 aa） Chain D 1–148（148 aa）	Not recorded	V91 N-(5-{3-[(2S)-1,3-thiazolidin-2-yl]azetidine-1-carbonyl}thiophen-2-yl)-L-prolinamide × 4 EDO 1,2-ETHANEDIOL × 6 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；277 K；0.1 M Tris, pH 7.3, 0.2 M magnesium chloride, 2.2 M sodium chloride	Resolution 2.10 Å R-free 0.264
8I60 Crystal structure of GAS41 YEATS domain in complex with histone H3K27cr Deposited 2023-01-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 11–150（140 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；Ammonium sulfate	Resolution 2.30 Å R-free 0.291
8I60 Crystal structure of GAS41 YEATS domain in complex with histone H3K27cr Deposited 2023-01-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 11–150（140 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；Ammonium sulfate	Resolution 2.30 Å R-free 0.291
8IIY Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide Deposited 2023-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 19–159（141 aa）	Mutation：D108A, K109A, E198A, N199A, K265A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide	Resolution 2.15 Å R-free 0.247
8IIZ Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac peptide Deposited 2023-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 19–159（141 aa）	Mutation：D108A, K109A, E198A, N199A, K265A	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide	Resolution 2.10 Å R-free 0.301
8IJ0 Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide Deposited 2023-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 19–159（141 aa）	Not recorded	GOL GLYCEROL × 3 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Na-HEPES buffer (pH 7.5) containing 5% (w/v) PEG 400 and 2 M ammonium sulfate	Resolution 1.52 Å R-free 0.189
8IJ0 Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide Deposited 2023-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 19–159（141 aa）	Not recorded	GOL GLYCEROL × 3 SO4 SULFATE ION × 4 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Na-HEPES buffer (pH 7.5) containing 5% (w/v) PEG 400 and 2 M ammonium sulfate	Resolution 1.52 Å R-free 0.189
8X15 Structure of nucleosome-bound SRCAP-C in the apo state Deposited 2023-11-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain W 1–227（227 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8X19 Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state Deposited 2023-11-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain W 1–227（227 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8X1C Structure of nucleosome-bound SRCAP-C in the ADP-bound state Deposited 2023-11-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain W 1–227（227 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9O4Y GAS41 YEATS domain in complex with DLG-1 Deposited 2025-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–148（148 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 A1B9P N-[5-(3-{(5M)-5-[3-(aminomethyl)phenyl]-1,3-thiazol-2-yl}azetidine-1-carbonyl)thiophen-2-yl]-L-prolinamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；1260 mM Ammonium sulfate, 100 mM HEPES, pH 7.5, 25% Glycerol	Resolution 2.30 Å R-free 0.258
9O4Y GAS41 YEATS domain in complex with DLG-1 Deposited 2025-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	A1B9P N-[5-(3-{(5M)-5-[3-(aminomethyl)phenyl]-1,3-thiazol-2-yl}azetidine-1-carbonyl)thiophen-2-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；1260 mM Ammonium sulfate, 100 mM HEPES, pH 7.5, 25% Glycerol	Resolution 2.30 Å R-free 0.258
9O4Y GAS41 YEATS domain in complex with DLG-1 Deposited 2025-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–148（148 aa）	Not recorded	A1B9P N-[5-(3-{(5M)-5-[3-(aminomethyl)phenyl]-1,3-thiazol-2-yl}azetidine-1-carbonyl)thiophen-2-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；1260 mM Ammonium sulfate, 100 mM HEPES, pH 7.5, 25% Glycerol	Resolution 2.30 Å R-free 0.258
9O4Y GAS41 YEATS domain in complex with DLG-1 Deposited 2025-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–148（148 aa）	Not recorded	A1B9P N-[5-(3-{(5M)-5-[3-(aminomethyl)phenyl]-1,3-thiazol-2-yl}azetidine-1-carbonyl)thiophen-2-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；1260 mM Ammonium sulfate, 100 mM HEPES, pH 7.5, 25% Glycerol	Resolution 2.30 Å R-free 0.258
9X8S Crystal structure of the human GAS41 YEATS domain in complex with an acetylated YFV capsid peptide (K4ac) Deposited 2025-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 15–146（132 aa） Chain B 15–146（132 aa） Chain C 15–146（132 aa） Chain D 15–146（132 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Sodium sulfate , Bis-Tris propane (pH= 6.5), PEG 3350	Resolution 1.70 Å R-free 0.206
9X8U Crystal structure of the human GAS41 YEATS domain in complex with an acetylated YFV capsid peptide (K8ac) Deposited 2025-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 15–145（131 aa） Chain B 15–145（131 aa） Chain C 15–145（131 aa） Chain D 15–145（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Sodium sulfate , Bis-Tris propane (pH= 6.5), PEG 3350	Resolution 3.00 Å R-free 0.266

18 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YETS4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149 Author chain B； PDBConstruct 1–149； UniProt 1–149 Author chain C； PDBConstruct 1–149； UniProt 1–149 Author chain D； PDBConstruct 1–149； UniProt 1–149 Author chain E； PDBConstruct 1–149； UniProt 1–149 Author chain F； PDBConstruct 1–149； UniProt 1–149 Author chain G； PDBConstruct 1–149； UniProt 1–149 Author chain H； PDBConstruct 1–149； UniProt 1–149

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	8dkb
Deposition date deposition_date	2022-07-05
Structure title title	Crystal Structure of human YEATS4 in complex with Pfizer small molecule compound 3b
Keywords keywords	protein binding, histone binding, lysine-acetylated histone binding; PROTEIN BINDING
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	37.82 Å
Radius of gyration Rg (electron density) rg_electron	37.00 Å
Forward intensity I(0) i0	195323000.00
Molecular weight molecular_weight	122080.0 kDa
Excluded volume excluded_volume	156530 Å³
Envelope volume envelope_volume	220780 Å³
Hydration-shell volume shell_volume	49934 Å³
Envelope diameter envelope_diameter	124.7 Å
Shell Rg shell_rg	43.15 Å
Envelope Rg envelope_rg	36.04 Å
Shape Rg shape_rg	36.98 Å
Total Rg total_rg	37.56 Å
Total atoms total_atoms	8662
Residues n_residues	1011
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	120.2 Å
Rg (real space) rg_real	37.65 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	1.9530e+08
I(0) uncertainty (real space) i0_real_error	3.2080e+06
Rg (reciprocal space) rg_reciprocal	37.76 Å
I(0) (reciprocal space) i0_reciprocal	195300000.0000
Solution quality estimate total_estimate	0.9009
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.9 Å
Skewness Skewness skewness	0.139
Kurtosis Kurtosis kurtosis	-0.576
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19830000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.927

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	YEATS domain-containing protein 4
Molecular weight formula_weight	18230.9 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	8996

MFKRMAEFGPDSGGRVKGVTIVKPIVYGNVARYFGKKREEDGHTHQWTVYVKPYRNEDMSAYVKKIQFKLHESYGNPLRVVTKPPYEITETGWGEFEIIIKIFFIDPNERPVTLYHLLKLFQSDTNAMLGKKTVVSEFYDEMIFQDPTAHHHHHH

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	N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide
Molecular weight formula_weight	412.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	334

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8. Citations (1)

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Unit-cell length a length_a	60.600 Å
Unit-cell length b length_b	109.300 Å
Unit-cell length c length_c	103.830 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.68 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.580 Å
Low-resolution limit resolution_low	41.300 Å
R factor r_factor	0.1740
R_work r_work	0.1710
R_free r_free	0.2260

fit	/app/data/saxs_computation/dk/8dkb/8dkb.fit
pddf	/app/data/pr_computation/dk/8dkb/8dkb.pr.out
profile	/app/data/saxs_computation/dk/8dkb/8dkb.dat