SAXSdb — 6j68

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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 Serine/threonine-protein kinase LATS1 × 1 （Q8BYR2）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 5–132	Not recorded	Peptide from Serine/threonine-protein kinase LATS1 × 1 （Q8BYR2）	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

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 6J68	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6J69 Structure of KIBRA and Dendrin 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 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 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 5 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 Author chain B； PDBConstruct 7–134； UniProt 5–132

Peptide from Serine/threonine-protein kinase LATS1

Mus musculus

UniProt Q8BYR2

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 C； UniProt 545–568	Not recorded	Protein KIBRA × 1 （Q5SXA9）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 545–568	Not recorded	Protein KIBRA × 1 （Q5SXA9）	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

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 6J68	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5B6B Complex of LATS1 and phosphomimetic MOB1b Deposited 2016-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 621–703（83 aa） Fragment：UNP residues 621-703 Chain J 621–703（83 aa） Fragment：UNP residues 621-703	Not recorded	CL CHLORIDE ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, sodium sulfate	Resolution 3.54 Å R-free 0.266
5B6B Complex of LATS1 and phosphomimetic MOB1b Deposited 2016-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 621–703（83 aa） Fragment：UNP residues 621-703 Chain L 621–703（83 aa） Fragment：UNP residues 621-703	Not recorded	CL CHLORIDE ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, sodium sulfate	Resolution 3.54 Å R-free 0.266
5B6B Complex of LATS1 and phosphomimetic MOB1b Deposited 2016-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 621–703（83 aa） Fragment：UNP residues 621-703 Chain I 621–703（83 aa） Fragment：UNP residues 621-703	Not recorded	CL CHLORIDE ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, sodium sulfate	Resolution 3.54 Å R-free 0.266
5B6B Complex of LATS1 and phosphomimetic MOB1b Deposited 2016-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 621–703（83 aa） Fragment：UNP residues 621-703 Chain P 621–703（83 aa） Fragment：UNP residues 621-703	Not recorded	CL CHLORIDE ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, sodium sulfate	Resolution 3.54 Å R-free 0.266

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

View Construct and Data Evidence

UniProt name	LATS1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–28； UniProt 545–568 Author chain D； PDBConstruct 5–28； UniProt 545–568

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	6j68
Deposition date deposition_date	2019-01-14
Structure title title	Structure of KIBRA and LATS1 Complex
Keywords keywords	Tandem WW domain, Tandem PY motif, HIPPO Signaling, CELL CYCLE; CELL CYCLE
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	45.37 Å
Radius of gyration Rg (electron density) rg_electron	46.36 Å
Forward intensity I(0) i0	15158600.00
Molecular weight molecular_weight	30848.0 kDa
Excluded volume excluded_volume	38297 Å³
Envelope volume envelope_volume	73916 Å³
Hydration-shell volume shell_volume	15377 Å³
Envelope diameter envelope_diameter	140.7 Å
Shell Rg shell_rg	43.40 Å
Envelope Rg envelope_rg	43.28 Å
Shape Rg shape_rg	46.46 Å
Total Rg total_rg	45.81 Å
Total atoms total_atoms	2190
Residues n_residues	276
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	132.9 Å
Rg (real space) rg_real	46.20 Å
Rg uncertainty (real space) rg_real_error	1.37 Å
I(0) (real space) i0_real	1.5160e+07
I(0) uncertainty (real space) i0_real_error	2.7740e+05
Rg (reciprocal space) rg_reciprocal	45.38 Å
I(0) (reciprocal space) i0_reciprocal	15140000.0000
Solution quality estimate total_estimate	0.5585
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.0 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-1.195
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	489200.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.084; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.006; Smooth: 0.000

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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	Protein KIBRA
Molecular weight formula_weight	16036.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2270

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 Serine/threonine-protein kinase LATS1
Molecular weight formula_weight	2926.2 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPGSVAEAPSYQGPPPPYPKHLLHQNPS

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	80

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8. Citations (1)

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Unit-cell length a length_a	44.314 Å
Unit-cell length b length_b	62.837 Å
Unit-cell length c length_c	156.823 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.495 Å
Low-resolution limit resolution_low	49.035 Å
R factor r_factor	0.2246
R_work r_work	0.2220
R_free r_free	0.2740

fit	/app/data/saxs_computation/j6/6j68/6j68.fit
pddf	/app/data/pr_computation/j6/6j68/6j68.pr.out
profile	/app/data/saxs_computation/j6/6j68/6j68.dat

Structure of KIBRA and LATS1 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 Serine/threonine-protein kinase LATS1

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)