SAXSdb — 6j69

▼

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 Dendrin × 1 （Q80TS7）	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

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 6J69	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 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 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
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 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 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
6JJY Crystal Structure of KIBRA and beta-Dystroglycan 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	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

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 Dendrin

Mus musculus

UniProt Q80TS7

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 B； UniProt 222–246	Not recorded	Protein KIBRA × 1 （Q5SXA9）	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

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 6J69	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6JJZ Crystal Structure of MAGI2 and Dendrin complex Deposited 2019-02-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 222–235（14 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；289 K；2.0-2.5M ammonium sulfate, 100mM sodium acetate (pH 4.6)	Resolution 1.65 Å R-free 0.238
6JJZ Crystal Structure of MAGI2 and Dendrin complex Deposited 2019-02-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 222–235（14 aa）	Not recorded	ACT ACETATE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；289 K；2.0-2.5M ammonium sulfate, 100mM sodium acetate (pH 4.6)	Resolution 1.65 Å R-free 0.238
6JK0 Crystal Structure of YAP1 and Dendrin complex Deposited 2019-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 222–241（20 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；25-30% w/v PEG400, 200mM CaCl2, 100mM HEPS (pH 7.5)	Resolution 3.10 Å R-free 0.243
6JK1 Crystal Structure of YAP1 and Dendrin complex 2 Deposited 2019-02-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 222–241（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；28-35% w/v pentaerythritol propoxylat 426 (5/4 PO/OH), 100mM HEPES (pH 7.5)	Resolution 2.00 Å R-free 0.211
6JK1 Crystal Structure of YAP1 and Dendrin complex 2 Deposited 2019-02-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 222–241（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；28-35% w/v pentaerythritol propoxylat 426 (5/4 PO/OH), 100mM HEPES (pH 7.5)	Resolution 2.00 Å R-free 0.211
6KKG Crystal structure of MAGI2-Dendrin complex Deposited 2019-07-25	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 222–241（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.2M Ammonium Sulfate, 150mM Malate at pH 5.1, 4.0% v/v 1,2-Propanedio	Resolution 2.15 Å R-free 0.264
6KKG Crystal structure of MAGI2-Dendrin complex Deposited 2019-07-25	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 222–241（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.2M Ammonium Sulfate, 150mM Malate at pH 5.1, 4.0% v/v 1,2-Propanedio	Resolution 2.15 Å R-free 0.264
7BQG Complex structure of SAV1 and Dendrin Deposited 2020-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 224–235（12 aa）	Not recorded	K POTASSIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；2% w/v PEG 2000 MME and 100 mM BIS-TRIS propane (pH 9.0)	Resolution 1.55 Å R-free 0.217

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

View Construct and Data Evidence

UniProt name	DEND_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–25； UniProt 222–246

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	6j69
Deposition date deposition_date	2019-01-14
Structure title title	Structure of KIBRA and Dendrin Complex
Keywords keywords	Tandem WW domain, Tandem PY motif, HIPPO Signaling, CELL CYCLE; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	28.07 Å
Radius of gyration Rg (electron density) rg_electron	27.85 Å
Forward intensity I(0) i0	4864300.00
Molecular weight molecular_weight	16125.0 kDa
Excluded volume excluded_volume	19983 Å³
Envelope volume envelope_volume	32509 Å³
Hydration-shell volume shell_volume	11411 Å³
Envelope diameter envelope_diameter	95.6 Å
Shell Rg shell_rg	29.95 Å
Envelope Rg envelope_rg	27.16 Å
Shape Rg shape_rg	27.87 Å
Total Rg total_rg	28.09 Å
Total atoms total_atoms	1145
Residues n_residues	142
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	91.9 Å
Rg (real space) rg_real	28.34 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	4.8640e+06
I(0) uncertainty (real space) i0_real_error	8.3790e+04
Rg (reciprocal space) rg_reciprocal	28.26 Å
I(0) (reciprocal space) i0_reciprocal	4864000.0000
Solution quality estimate total_estimate	0.7483
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.4 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.808
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	203900.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.512; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.431; Smooth: 0.756

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

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	1158

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 K-12

Entity 2 Entity 2 polymer

Description description	Peptide from Dendrin
Molecular weight formula_weight	2751.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DRPPPYVAPPSYEGPHRTLGTKRGP

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 K-12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

▶

8. Citations (1)

▶

Unit-cell length a length_a	85.443 Å
Unit-cell length b length_b	85.443 Å
Unit-cell length c length_c	80.566 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 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.753 Å
Low-resolution limit resolution_low	42.721 Å
R factor r_factor	0.2386
R_work r_work	0.2361
R_free r_free	0.2824

fit	/app/data/saxs_computation/j6/6j69/6j69.fit
pddf	/app/data/pr_computation/j6/6j69/6j69.pr.out
profile	/app/data/saxs_computation/j6/6j69/6j69.dat

Structure of KIBRA and Dendrin Complex

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 Dendrin

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)