SAXSdb — 7tyg

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

Leucine-rich repeat protein SHOC-2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 80–582	Fragment：residues 80-582	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.1M Tris-Cl(8.0), 0.2 M MgCl2, 11% PEG4K, 2.5% 1,5-diaminopentane	Resolution 1.90 Å R-free 0.226
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 80–582	Fragment：residues 80-582	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.1M Tris-Cl(8.0), 0.2 M MgCl2, 11% PEG4K, 2.5% 1,5-diaminopentane	Resolution 1.90 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 7TYG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SD0 Cryo-EM structure of the SHOC2:PP1C:MRAS complex Deposited 2021-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–582（581 aa）	Not recorded	GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Used the "perpetually hydrated" method of applying graphene oxide. (Cheung et al., 2018)	Resolution 2.95 Å
7SD1 Crystal structure of SHOC2 Deposited 2021-09-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–582（581 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；100 mM Tris 8.5, 200 mM MgCl2, 14% (w/v) PEG 4000	Resolution 3.19 Å R-free 0.238
7SD1 Crystal structure of SHOC2 Deposited 2021-09-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–582（581 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；100 mM Tris 8.5, 200 mM MgCl2, 14% (w/v) PEG 4000	Resolution 3.19 Å R-free 0.238
7SD1 Crystal structure of SHOC2 Deposited 2021-09-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–582（581 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；100 mM Tris 8.5, 200 mM MgCl2, 14% (w/v) PEG 4000	Resolution 3.19 Å R-free 0.238
7SD1 Crystal structure of SHOC2 Deposited 2021-09-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–582（581 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；100 mM Tris 8.5, 200 mM MgCl2, 14% (w/v) PEG 4000	Resolution 3.19 Å R-free 0.238
7T7A Crystal Structure of Human SHOC2: A Leucine-Rich Repeat Protein Deposited 2021-12-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 88–581（494 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；400 mM magnesium nitrate 200 mM Tris PH 8.5 23-30% PEG 4K	Resolution 1.79 Å R-free 0.241
7T7A Crystal Structure of Human SHOC2: A Leucine-Rich Repeat Protein Deposited 2021-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 88–581（494 aa）	Not recorded	NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；400 mM magnesium nitrate 200 mM Tris PH 8.5 23-30% PEG 4K	Resolution 1.79 Å R-free 0.241
7TVF Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom Deposited 2022-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 2–582（581 aa）	Not recorded	GOL GLYCEROL × 7 SO4 SULFATE ION × 5 MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Crystals originally grown in 15% PEG 1500, 0.1M MIB pH 4.2 (15mg/ml of SMP) were used to make seeds. Microseeded into a condition with a reservoir consisting of 17.8% PEG 3350, 136mM sodium sulfate with 1:10 dilution of seeds (7.5mg/ml of SMP) using a ratio of 200nl protein:133nl reservoir:67nl diluted seeds	Resolution 2.17 Å R-free 0.226
7TVF Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom Deposited 2022-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–582（581 aa）	Not recorded	GOL GLYCEROL × 6 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 2 CL CHLORIDE ION × 3 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Crystals originally grown in 15% PEG 1500, 0.1M MIB pH 4.2 (15mg/ml of SMP) were used to make seeds. Microseeded into a condition with a reservoir consisting of 17.8% PEG 3350, 136mM sodium sulfate with 1:10 dilution of seeds (7.5mg/ml of SMP) using a ratio of 200nl protein:133nl reservoir:67nl diluted seeds	Resolution 2.17 Å R-free 0.226
7TVG Crystal Structure of SHOC2 to a resolution of 2.4 Angstrom Deposited 2022-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 59–564（506 aa）	Not recorded	SO4 SULFATE ION × 6 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.5M ammonium sulfate, 0.1M sodium citrate pH 5.0	Resolution 2.40 Å R-free 0.267
7TXH Human MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca Deposited 2022-02-09	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 80–582（503 aa）	Mutation：M173I	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 6 MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M NaH2PO4 pH 6.5, 12% PEG 8000	Resolution 1.95 Å R-free 0.210
7TXH Human MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca Deposited 2022-02-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 80–582（503 aa）	Mutation：M173I	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 10 MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M NaH2PO4 pH 6.5, 12% PEG 8000	Resolution 1.95 Å R-free 0.210
7UPI Cryo-EM structure of SHOC2-PP1c-MRAS holophosphatase complex Deposited 2022-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–582（582 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；Fluorinated octyl maltoside added immediately prior to vitrification cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
9BTM NRas 1-169 Q61R in Complex with Shoc2 80-582 Deposited 2024-05-15	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 80–582（503 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.1 M Hepes pH 7, 15% PEG 4000	Resolution 2.73 Å R-free 0.238
9BTN Structure of human SHOC2 in complex with a cyclic peptide Deposited 2024-05-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 80–582（503 aa） Fragment：residues 80-582	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.05 M Hepes pH 7.5, 35% v/v pentaerythritol propoxylate 5/4 PO/OH (PP 5/4 PO/OH), 0.2M KCl	Resolution 2.04 Å R-free 0.252
9BTP Structure of human SHOC2 in complex with a small molecule inhibitor (S)-5 Deposited 2024-05-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 80–582（503 aa） Fragment：residues 80-582	Not recorded	A1ATZ (2S)-{2-[(4-chloro[1,1'-biphenyl]-3-yl)methoxy]phenyl}[(2-oxo-2,3-dihydro-1,3-benzoxazol-5-yl)amino]acetic acid × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；See reference. Crystals of apo SHOC2 in space group p212121 were incubated with compound and harvested. 50 mM Tris pH 7.0, 200 mM KCl, 40% PP 5/4 PO/OH	Resolution 2.37 Å R-free 0.263
9O65 Cryo-EM structure of SHOC2-KRAS-PP1CA (SKP) complex Deposited 2025-04-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–582（582 aa）	Mutation：M173I	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9OVJ Structure of human SHOC2 in complex with a small molecule inhibitor (R)-5 Deposited 2025-05-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 80–582（503 aa） Fragment：residues 80-582	Not recorded	A1CF1 (2R)-{2-[(4-chloro[1,1'-biphenyl]-3-yl)methoxy]phenyl}[(2-oxo-2,3-dihydro-1,3-benzoxazol-5-yl)amino]acetic acid × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；See reference. Crystals of apo SHOC2 in space group p212121 were incubated with compound and harvested. 0.05 M Tris (7.0), 40% (v/v) Pentaerythritol Propoxylate 5/4 PO/OH, 0.2 M KCl	Resolution 2.68 Å R-free 0.275

12 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SHOC2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–505； UniProt 80–582 Author chain B； PDBConstruct 3–505； UniProt 80–582

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	7tyg
Deposition date deposition_date	2022-02-13
Structure title title	Structure of the human leucine rich repeat protein SHOC2, residues 80-582
Keywords keywords	RAS, PP1, SHOC2, LRR, HYDROLASE; HYDROLASE
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	32.74 Å
Radius of gyration Rg (electron density) rg_electron	31.91 Å
Forward intensity I(0) i0	184428000.00
Molecular weight molecular_weight	111030.0 kDa
Excluded volume excluded_volume	140560 Å³
Envelope volume envelope_volume	184330 Å³
Hydration-shell volume shell_volume	47179 Å³
Envelope diameter envelope_diameter	105.7 Å
Shell Rg shell_rg	39.91 Å
Envelope Rg envelope_rg	31.34 Å
Shape Rg shape_rg	31.89 Å
Total Rg total_rg	32.66 Å
Total atoms total_atoms	7789
Residues n_residues	987
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	101.5 Å
Rg (real space) rg_real	32.52 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	1.8440e+08
I(0) uncertainty (real space) i0_real_error	2.4810e+06
Rg (reciprocal space) rg_reciprocal	32.62 Å
I(0) (reciprocal space) i0_reciprocal	184400000.0000
Solution quality estimate total_estimate	0.8942
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	44.4 Å
Skewness Skewness skewness	0.130
Kurtosis Kurtosis kurtosis	-0.415
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0006
Highest regularization parameter α highest_alpha	42560000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.954

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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	Leucine-rich repeat protein SHOC-2
Molecular weight formula_weight	56737.6 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	8414

GPGTRKKSSNAEVIKELNKCREENSMRLDLSKRSIHILPSSIKELTQLTELYLYSNKLQSLPAEVGCLVNLMTLALSENSLTSLPDSLDNLKKLRMLDLRHNKLREIPSVVYRLDSLTTLYLRFNRITTVEKDIKNLSKLSMLSIRENKIKQLPAEIGELCNLITLDVAHNQLEHLPKEIGNCTQITNLDLQHNELLDLPDTIGNLSSLSRLGLRYNRLSAIPRSLAKCSALEELNLENNNISTLPESLLSSLVKLNSLTLARNCFQLYPVGGPSQFSTIYSLNMEHNRINKIPFGIFSRAKVLSKLNMKDNQLTSLPLDFGTWTSMVELNLATNQLTKIPEDVSGLVSLEVLILSNNLLKKLPHGLGNLRKLRELDLEENKLESLPNEIAYLKDLQKLVLTNNQLTTLPRGIGHLTNLTHLGLGENLLTHLPEEIGTLENLEELYLNDNPNLHSLPFELALCSKLSIMSIENCPLSHLPPQIVAGGPSFIIQFLKMQGPYRAMV

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	625

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8. Citations (1)

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Unit-cell length a length_a	91.350 Å
Unit-cell length b length_b	102.880 Å
Unit-cell length c length_c	120.830 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	41.440 Å
R factor r_factor	0.1898
R_work r_work	0.1879
R_free r_free	0.2258

fit	/app/data/saxs_computation/ty/7tyg/7tyg.fit
pddf	/app/data/pr_computation/ty/7tyg/7tyg.pr.out
profile	/app/data/saxs_computation/ty/7tyg/7tyg.dat

Structure of the human leucine rich repeat protein SHOC2, residues 80-582

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

Leucine-rich repeat protein SHOC-2

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