SAXSdb — 6bph

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

AT-rich interactive domain-containing protein 4A

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 568–635	Not recorded	UNX UNKNOWN LIGAND × 34	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG 3350, 0.2M magnesium chloride, 0.1M HEPES, pH 7.5	Resolution 1.85 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 6BPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LCC Solution structure of RBBP1 chromobarrel domain Deposited 2011-04-28	Different construct Different oligomeric state 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 568–635（68 aa） Fragment：UNP RESIDUES 568-635	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient NMR sample composition 0.5 mM [U-95% 15N] entity-1, 50 mM sodium phosphate-2, 50 mM sodium chloride-3, 5 mM DTT-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-95% 13C; U-95% 15N] entity-5, 50 mM sodium phosphate-6, 50 mM sodium chloride-7, 5 mM DTT-8, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MAM Solution structure of the interdigitated double Tudor domain of RBBP1 Deposited 2013-07-15	Different construct Different oligomeric state 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 4–121（118 aa） Fragment：UNP RESIDUES 4-121	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 0.6 mM [U-95% 13C; U-95% 15N] entity-1, 10 % [U-99% 2H] D2O-2, 0.0004 % DSS-3, 15 mM DTT-4, 50 mM sodium chloride-5, 50 mM TRIS-6, 2 mM EDTA-7, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YRV Solution structure of the RBB1NT domain of human RB(retinoblastoma)-binding protein 1 Deposited 2007-04-03	Different construct Different oligomeric state 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 170–273（104 aa） Fragment：UNP region 170-273	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.2mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
6L87 Solution structure of the tandem PWWP-ARID domains of human RBBP1 Deposited 2019-11-05	Different construct Different oligomeric state 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 171–414（244 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；302 K；Ionic strength (raw mmCIF value) 720；Pressure 1 NMR sample composition 10 mM sodium phosphate, 700 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium phosphate, 700 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7SMC p107 pocket domain complexed with ARID4A peptide Deposited 2021-10-25	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 B 953–967（15 aa） Fragment：UNP residues 953-967	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 2.70 Å R-free 0.298
7SMC p107 pocket domain complexed with ARID4A peptide Deposited 2021-10-25	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 953–967（15 aa） Fragment：UNP residues 953-967	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 2.70 Å R-free 0.298
7V8N Crystal structure of the PWWP-ARID domain of ARID4A Deposited 2021-08-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 169–417（249 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris pH8.0	Resolution 2.05 Å R-free 0.231
7V8N Crystal structure of the PWWP-ARID domain of ARID4A Deposited 2021-08-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 169–417（249 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris pH8.0	Resolution 2.05 Å R-free 0.231

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARI4A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–69； UniProt 568–635

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	6bph
Deposition date deposition_date	2017-11-23
Structure title title	Crystal structure of the chromodomain of RBBP1
Keywords keywords	Crystal structure of the chromodomain of RBBP1, Structural Genomics, Structural Genomics Consortium, SGC, UNKNOWN FUNCTION; UNKNOWN FUNCTION
Experimental Method method	X-RAY DIFFRACTION

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

该条目暂无 SAXS 数据。

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

该条目暂无 P(r) 分析数据。

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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	AT-rich interactive domain-containing protein 4A
Molecular weight formula_weight	8068.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	578

GEDMEPCLTGTKVKVKYGRGKTQKIYEASIKSTEIDDGEVLYLVHYYGWNVRYDEWVKADRIIWPLDKG

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	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	17

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	24

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6bphA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

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8. Citations (1)

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Unit-cell length a length_a	41.493 Å
Unit-cell length b length_b	41.493 Å
Unit-cell length c length_c	81.349 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	36.900 Å
R factor r_factor	0.2070
R_work r_work	0.2060
R_free r_free	0.2260

Crystal structure of the chromodomain of RBBP1