SAXSdb — 6jjy

▼

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

Protein KIBRA

Mus musculus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 5–132	Not recorded	Peptide from Dystroglycan × 1 （Q14118） SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；3.0-4.0M NaCl, 100mM Bis-Tris (pH 6.5)	Resolution 2.30 Å R-free 0.253

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 6JJY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6J68 Structure of KIBRA and LATS1 Complex Deposited 2019-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 5–132（128 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；289 K；0.1M Tris, 28% PEG 4000	Resolution 2.50 Å R-free 0.274
6J68 Structure of KIBRA and LATS1 Complex Deposited 2019-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 5–132（128 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；289 K；0.1M Tris, 28% PEG 4000	Resolution 2.50 Å R-free 0.274
6J69 Structure of KIBRA and Dendrin Complex Deposited 2019-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 5–132（128 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；0.1M HEPES, 0.4M Sodium citrate, 16% 2-Propanol	Resolution 2.75 Å R-free 0.282
6JJW Crystal Structure of KIBRA and PTPN14 complex Deposited 2019-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 5–132（128 aa）	Not recorded	CL CHLORIDE ION × 8 FMT FORMIC ACID × 3 GOL GLYCEROL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；700mM magnesium formate, 100mM Bis-Tris Propane (pH 7.0)	Resolution 2.40 Å R-free 0.242
6JJX Crystal Structure of KIBRA and Angiomotin complex Deposited 2019-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 5–132（128 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；25% w/v pentaerythritol propoxylat 629 (17/8 PO/OH), 50mM MgCl2, 100mM Tris (pH 8.5)	Resolution 2.00 Å R-free 0.234
6JJX Crystal Structure of KIBRA and Angiomotin complex Deposited 2019-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 5–132（128 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；25% w/v pentaerythritol propoxylat 629 (17/8 PO/OH), 50mM MgCl2, 100mM Tris (pH 8.5)	Resolution 2.00 Å R-free 0.234

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

View Construct and Data Evidence

UniProt name	KIBRA_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–134； UniProt 5–132

Peptide from Dystroglycan

Homo sapiens

UniProt Q14118

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain U； UniProt 877–895	Not recorded	Protein KIBRA × 1 （Q5SXA9） SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；3.0-4.0M NaCl, 100mM Bis-Tris (pH 6.5)	Resolution 2.30 Å R-free 0.253

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 6JJY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EG4 STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BETA-DYSTROGLYCAN PEPTIDE Deposited 2000-02-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 881–895（15 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；ammonium sulfate, glycerol, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.249
2MK7 Tetra-O-GalNAc glycosylated mucin sequence from alpha dystroglycan mucin domain Deposited 2014-02-02	Different construct Different mutation/modification 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 419–427（9 aa） Fragment：mucin domain peptide (UNP residues 419-427)	Non-standard monomer：Yes (specific site not provided by mmCIF)	A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 4	SOLUTION NMR NMR measurement conditions pH 4.5；288 K；Pressure ambient NMR sample composition 2-10 mM aDG mucin domain peptide, 100% D2O \| 100% D2O NMR sample composition 2-10 mM aDG mucin domain peptide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
5GGP Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta1,2-Man-peptide Deposited 2016-06-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 316–325（10 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；MES-NaOH, LiCl2, Na acetate, PEG-6000	Resolution 1.60 Å R-free 0.246
5GGP Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta1,2-Man-peptide Deposited 2016-06-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 316–325（10 aa）	Not recorded	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；MES-NaOH, LiCl2, Na acetate, PEG-6000	Resolution 1.60 Å R-free 0.246
5LLK Crystal structure of human alpha-dystroglycan Deposited 2016-07-27	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 52–315（264 aa） Fragment：UNP residues 52-315	Mutation：R168H	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；0.8 M Sodium Citrate	Resolution 1.80 Å R-free 0.195
8UF4 Crystal structure of wildtype dystroglycan proteolytic domain (juxtamembrane domain) Deposited 2023-10-03	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 491–653（163 aa） Fragment：residues 491-653 Chain B 654–748（95 aa） Fragment：residues 654-748 Chain C 491–653（163 aa） Fragment：residues 491-653 Chain D 654–748（95 aa） Fragment：residues 654-748	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；295 K；0.1 M Tris, 0.2 M lithium sulfate, 20% PEG 4000	Resolution 2.43 Å R-free 0.275

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

View Construct and Data Evidence

UniProt name	DAG1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain U； PDBConstruct 3–21； UniProt 877–895

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	6jjy
Deposition date deposition_date	2019-02-27
Structure title title	Crystal Structure of KIBRA and beta-Dystroglycan
Keywords keywords	WW tandem, PY tandem, KIBRA, PTPN14, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	26.87 Å
Radius of gyration Rg (electron density) rg_electron	27.93 Å
Forward intensity I(0) i0	5492060.00
Molecular weight molecular_weight	17030.0 kDa
Excluded volume excluded_volume	21023 Å³
Envelope volume envelope_volume	31339 Å³
Hydration-shell volume shell_volume	11513 Å³
Envelope diameter envelope_diameter	102.2 Å
Shell Rg shell_rg	28.20 Å
Envelope Rg envelope_rg	29.30 Å
Shape Rg shape_rg	27.92 Å
Total Rg total_rg	27.98 Å
Total atoms total_atoms	1203
Residues n_residues	145
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	103.5 Å
Rg (real space) rg_real	27.88 Å
Rg uncertainty (real space) rg_real_error	1.44 Å
I(0) (real space) i0_real	5.4920e+06
I(0) uncertainty (real space) i0_real_error	9.0450e+04
Rg (reciprocal space) rg_reciprocal	27.57 Å
I(0) (reciprocal space) i0_reciprocal	5491000.0000
Solution quality estimate total_estimate	0.6477
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	19.3 Å
Skewness Skewness skewness	0.837
Kurtosis Kurtosis kurtosis	-0.172
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	344100.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.155; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.005; Smooth: 0.946

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein KIBRA
Molecular weight formula_weight	16036.6 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	1289

GPGSEFELPLPEGWEEARDFDGKVYYIDHRNRTTSWIDPRDRYTKPLTFADCISDELPLGWEEAYDPQVGDYFIDHNTKTTQIEDPRVQWRREQEHMLKDYLVVAQEALSAQKEIYQVKQQRLELAQQEYQQLH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptide from Dystroglycan
Molecular weight formula_weight	2298.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

GPGSRPKNMTPYRSPPPYVPP

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 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	75

▶

8. Citations (1)

▶

Unit-cell length a length_a	73.483 Å
Unit-cell length b length_b	73.483 Å
Unit-cell length c length_c	105.322 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	2.298 Å
Low-resolution limit resolution_low	40.571 Å
R factor r_factor	0.2103
R_work r_work	0.2056
R_free r_free	0.2529

fit	/app/data/saxs_computation/jj/6jjy/6jjy.fit
pddf	/app/data/pr_computation/jj/6jjy/6jjy.pr.out
profile	/app/data/saxs_computation/jj/6jjy/6jjy.dat

Crystal Structure of KIBRA and beta-Dystroglycan

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

Protein KIBRA

State in the Current Structure

Other States of the Same Protein in the Database

Peptide from Dystroglycan

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)