SAXSdb — 5yf4

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

MOB-like protein phocein

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 53–210	Fragment：UNP residues 53-210	Peptide from Serine/threonine-protein kinase 26 × 2 （Q9P289） ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.1M HEPES, pH 7.5, 30% PEG 1000	Resolution 1.90 Å R-free 0.198

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 5YF4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7K36 Cryo-EM structure of STRIPAK complex Deposited 2020-09-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain H 1–225（225 aa）	Not recorded	MN MANGANESE (II) ION × 2 ZN ZINC ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

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

View Construct and Data Evidence

UniProt name	PHOCN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–162； UniProt 53–210

Peptide from Serine/threonine-protein kinase 26

OrganismNot specified

UniProt Q9P289

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 B； UniProt 320–335	Non-standard monomer：Yes (specific site not provided by mmCIF)	MOB-like protein phocein × 2 （Q9Y3A3） ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.1M HEPES, pH 7.5, 30% PEG 1000	Resolution 1.90 Å R-free 0.198

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 5YF4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3GGF Crystal structure of human Serine/threonine-protein kinase MST4 in complex with an quinazolin Deposited 2009-02-27	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 1–300（300 aa） Fragment：protein kinase	Not recorded	CD CADMIUM ION × 4 GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；12%w/v PEG 3350; 0.005M CdCl2; 0.1M HEPES, pH7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 2.35 Å R-free 0.277
3GGF Crystal structure of human Serine/threonine-protein kinase MST4 in complex with an quinazolin Deposited 2009-02-27	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 1–300（300 aa） Fragment：protein kinase	Not recorded	CD CADMIUM ION × 3 GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；12%w/v PEG 3350; 0.005M CdCl2; 0.1M HEPES, pH7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 2.35 Å R-free 0.277
3GGF Crystal structure of human Serine/threonine-protein kinase MST4 in complex with an quinazolin Deposited 2009-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–300（300 aa） Fragment：protein kinase Chain B 1–300（300 aa） Fragment：protein kinase	Not recorded	CD CADMIUM ION × 7 GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；12%w/v PEG 3350; 0.005M CdCl2; 0.1M HEPES, pH7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 2.35 Å R-free 0.277
3W8I Crystal structure of CCM3 in complex with the C-terminal regulatory domain of MST4 Deposited 2013-03-13	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 B 346–416（71 aa） Fragment：UNP RESIDUES 346-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1M Bis-Tris, 25% PEG3350, 0.3M ammonium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
4FZA Crystal structure of MST4-MO25 complex Deposited 2012-07-06	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 B 18–297（280 aa） Fragment：Kinase domain, UNP residues 18-297	Mutation：D162A	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.1M Tris pH 8.0, 20% PEG 350 mme, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.15 Å R-free 0.252
4FZD Crystal structure of MST4-MO25 complex with WSF motif Deposited 2012-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 18–297（280 aa） Fragment：Kinase domain, UNP residues 18-297 Chain C 323–327（5 aa） Fragment：WSF motif, UNP residues 323-327	Mutation：D162A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.1M Tris pH 8.0, 18% PEG 350 mme, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.25 Å R-free 0.260
4FZF Crystal structure of MST4-MO25 complex with DKI Deposited 2012-07-06	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 B 18–297（280 aa） Fragment：Kinase domain, UNP residues 18-297	Mutation：D162A	DKI 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.1M Tris pH 8.0, 20% PEG 350 mme, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.64 Å R-free 0.309
4GEH Crystal structure of MST4 dimerization domain complex with PDCD10 Deposited 2012-08-02	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 B 325–413（89 aa） Fragment：Dimerization domain, UNP residues 325-413	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；2% v/v Tacsimate pH 6.0, 0.1M BIS-TRIS pH 6.5, 18% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.95 Å R-free 0.253
4GEH Crystal structure of MST4 dimerization domain complex with PDCD10 Deposited 2012-08-02	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 D 325–413（89 aa） Fragment：Dimerization domain, UNP residues 325-413	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；2% v/v Tacsimate pH 6.0, 0.1M BIS-TRIS pH 6.5, 18% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.95 Å R-free 0.253
5XY9 Structure of the MST4 and 14-3-3 complex Deposited 2017-07-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 314–325（12 aa） Fragment：UNP residues 314-325 Chain D 314–325（12 aa） Fragment：UNP residues 314-325	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.2M MgCl2, 0.1M Tris pH 8.5, 25% PEG 3350	Resolution 2.30 Å R-free 0.245
7B36 MST4 in complex with compound G-5555 Deposited 2020-11-28	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 1–300（300 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 59T 8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；solution: protein 12 mg/ml in buffer 25mM HEPES pH 7.5, 200 mM NaCl, 0.5mM TCEP, 5% glycerol reservoir: 28% PEG6000, 0.1M HEPES pH 7.5	Resolution 2.11 Å R-free 0.244
7B36 MST4 in complex with compound G-5555 Deposited 2020-11-28	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 C 1–300（300 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 59T 8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；solution: protein 12 mg/ml in buffer 25mM HEPES pH 7.5, 200 mM NaCl, 0.5mM TCEP, 5% glycerol reservoir: 28% PEG6000, 0.1M HEPES pH 7.5	Resolution 2.11 Å R-free 0.244

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STK26_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–16； UniProt 320–335

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	5yf4
Deposition date deposition_date	2017-09-20
Structure title title	A kinase complex MST4-MOB4
Keywords keywords	Kinase, Complex, Phosphorylation, PROTEIN BINDING; PROTEIN BINDING
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	15.48 Å
Radius of gyration Rg (electron density) rg_electron	14.30 Å
Forward intensity I(0) i0	5226550.00
Molecular weight molecular_weight	15888.0 kDa
Excluded volume excluded_volume	19640 Å³
Envelope volume envelope_volume	22356 Å³
Hydration-shell volume shell_volume	13121 Å³
Envelope diameter envelope_diameter	51.1 Å
Shell Rg shell_rg	20.35 Å
Envelope Rg envelope_rg	14.77 Å
Shape Rg shape_rg	14.31 Å
Total Rg total_rg	15.45 Å
Total atoms total_atoms	1105
Residues n_residues	138
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	52.5 Å
Rg (real space) rg_real	15.38 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	5.2270e+06
I(0) uncertainty (real space) i0_real_error	5.8710e+04
Rg (reciprocal space) rg_reciprocal	15.39 Å
I(0) (reciprocal space) i0_reciprocal	5227000.0000
Solution quality estimate total_estimate	0.8608
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.137
Kurtosis Kurtosis kurtosis	-0.304
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1013000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	MOB-like protein phocein
Molecular weight formula_weight	18938.7 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	1215

STMENIDKILEPPEGQDEGVWKYEHLRQFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSRVSIKESSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETFLCHRFTKFVMKYNLMSKDNLIVPI

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(DE3)

Entity 2 Entity 2 polymer

Description description	Peptide from Serine/threonine-protein kinase 26
Molecular weight formula_weight	2090.1 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

THPEWSFTTVRKKPDP

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 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

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8. Citations (1)

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Unit-cell length a length_a	88.469 Å
Unit-cell length b length_b	33.997 Å
Unit-cell length c length_c	61.023 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	122.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.897 Å
Low-resolution limit resolution_low	30.038 Å
R factor r_factor	0.1572
R_work r_work	0.1527
R_free r_free	0.1977

fit	/app/data/saxs_computation/yf/5yf4/5yf4.fit
pddf	/app/data/pr_computation/yf/5yf4/5yf4.pr.out
profile	/app/data/saxs_computation/yf/5yf4/5yf4.dat

A kinase complex MST4-MOB4

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

MOB-like protein phocein

State in the Current Structure

Other States of the Same Protein in the Database

Peptide from Serine/threonine-protein kinase 26

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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)