SAXSdb — 9pku

▼

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

YEATS domain-containing protein 2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 201–332 Chain C； UniProt 201–332	Not recorded	LS-131 peptide × 2 GOL GLYCEROL × 8 BZ2 1-benzofuran-2-carboxylic acid × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.8；291 K；2.0 M Sodium chloride, 0.1 M bis-tris propane pH 7.8	Resolution 2.88 Å R-free 0.251

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 9PKU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5IQL Crystal structure of YEATS2 YEATS bound to H3K27cr peptide Deposited 2016-03-11	Different construct Different mutation/modification 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 201–332（132 aa） Fragment：YEATS domain (UNP RESIDUES 201-332)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；0.1M Bis-Tris propane, 4.0 M NH4Ac, pH 7.0	Resolution 2.10 Å R-free 0.253
5XNV Crystal structure of YEATS2 YEATS bound to H3K27ac peptide Deposited 2017-05-24	Different construct Different mutation/modification 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 201–332（132 aa） Fragment：UNP RESIDUES 201-332	Not recorded	NH4 AMMONIUM ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；291 K；0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1M CAPS, pH 10	Resolution 2.70 Å R-free 0.266
6LSD Crystal Structure of YEATS domain of human YEATS2 in complex with H3K27bz peptide Deposited 2020-01-17	Different construct Different mutation/modification 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 201–332（132 aa） Fragment：YEATS domain of YEATS2	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1 M Bis-Tris, pH 9.0, 2.0M ammonium sulfate	Resolution 2.05 Å R-free 0.234
6LSD Crystal Structure of YEATS domain of human YEATS2 in complex with H3K27bz peptide Deposited 2020-01-17	Different construct Different mutation/modification 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 201–332（132 aa） Fragment：YEATS domain of YEATS2	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1 M Bis-Tris, pH 9.0, 2.0M ammonium sulfate	Resolution 2.05 Å R-free 0.234
7EIE Crystal structure of YEATS2 YEATS domain Deposited 2021-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 202–329（128 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl buffer (pH 8.5) containing 2 M NaCl	Resolution 1.67 Å R-free 0.202
7EIE Crystal structure of YEATS2 YEATS domain Deposited 2021-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 202–329（128 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl buffer (pH 8.5) containing 2 M NaCl	Resolution 1.67 Å R-free 0.202

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YETS2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–135； UniProt 201–332 Author chain C； PDBConstruct 4–135； UniProt 201–332

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pku
Deposition date deposition_date	2025-07-14
最后修订 last_revision	2026-01-07
Structure title title	Crystal Structure of YEATS domain of human YEATS2 in complex with LS-131 peptide
Keywords keywords	ATAC complex, YEATS2, chemical probe, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	23.54 Å
Radius of gyration Rg (electron density) rg_electron	22.94 Å
Forward intensity I(0) i0	36846900.00
Molecular weight molecular_weight	31188.0 kDa
Excluded volume excluded_volume	30058 Å³
Envelope volume envelope_volume	52732 Å³
Hydration-shell volume shell_volume	19953 Å³
Envelope diameter envelope_diameter	88.5 Å
Shell Rg shell_rg	28.70 Å
Envelope Rg envelope_rg	23.50 Å
Shape Rg shape_rg	22.93 Å
Total Rg total_rg	23.53 Å
Total atoms total_atoms	2370
Residues n_residues	270
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

▼

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

Maximum dimension Dmax dmax	91.3 Å
Rg (real space) rg_real	23.65 Å
Rg uncertainty (real space) rg_real_error	1.07 Å
I(0) (real space) i0_real	3.6850e+07
I(0) uncertainty (real space) i0_real_error	5.8610e+05
Rg (reciprocal space) rg_reciprocal	23.62 Å
I(0) (reciprocal space) i0_reciprocal	36850000.0000
Solution quality estimate total_estimate	0.7147
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.460
Kurtosis Kurtosis kurtosis	-0.161
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10770000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.578; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.552; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	YEATS domain-containing protein 2
Molecular weight formula_weight	16087.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2435

SHMTSRLFVKKTIVVGNVSKYIPPDKREENDQSTHKWMVYVRGSRREPSINHFVKKVWFFLHPSYKPNDLVEVREPPFHLTRRGWGEFPVRVQVHFKDSQNKRIDIIHNLKLDRTYTGLQTLGAETVVDVELHRH

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	LS-131 peptide
Molecular weight formula_weight	477.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

KSAPX

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	1-benzofuran-2-carboxylic acid
Molecular weight formula_weight	162.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

▶

8. Citations (1)

▶

Unit-cell length a length_a	174.399 Å
Unit-cell length b length_b	51.559 Å
Unit-cell length c length_c	54.381 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.880 Å
Low-resolution limit resolution_low	49.430 Å
R factor r_factor	0.2130
R_work r_work	0.2085
R_free r_free	0.2513

fit	/app/data/saxs_computation/pk/9pku/9pku.fit
pddf	/app/data/pr_computation/pk/9pku/9pku.pr.out
profile	/app/data/saxs_computation/pk/9pku/9pku.dat

Crystal Structure of YEATS domain of human YEATS2 in complex with LS-131 peptide

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

YEATS domain-containing protein 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)