SAXSdb — 5yxh

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

GTP-binding protein Rheb

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 2–169	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；25% w/v PEG 1500	Resolution 2.04 Å R-free 0.299
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–169	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；25% w/v PEG 1500	Resolution 2.04 Å R-free 0.299
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 2–169	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；25% w/v PEG 1500	Resolution 2.04 Å R-free 0.299
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 2–169	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；25% w/v PEG 1500	Resolution 2.04 Å R-free 0.299

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 5YXH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XTQ Structure of small GTPase human Rheb in complex with GDP Deposited 2004-10-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa） Fragment：GTPase domain	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；potassium dihydrogenphosphate, PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.257
1XTR Structure of small GTPase human Rheb in complex with GppNHp Deposited 2004-10-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa） Fragment：GTPase domain	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；potassium dihydrogenphosphate, PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.65 Å R-free 0.270
1XTS Structure of small GTPase human Rheb in complex with GTP Deposited 2004-10-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa） Fragment：GTPase domain	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；ammonium dihydrogenphosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.277
3SEA Structure of Rheb-Y35A mutant in GDP- and GMPPNP-bound forms Deposited 2011-06-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–169（167 aa） Fragment：G-domain	Mutation：Y35A	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris hydrochloride, 200 mM Sodium acetate trihydrate, 30% w/v Polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.214
3SEA Structure of Rheb-Y35A mutant in GDP- and GMPPNP-bound forms Deposited 2011-06-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 3–169（167 aa） Fragment：G-domain	Mutation：Y35A	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris hydrochloride, 200 mM Sodium acetate trihydrate, 30% w/v Polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.214
3SEA Structure of Rheb-Y35A mutant in GDP- and GMPPNP-bound forms Deposited 2011-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 3–169（167 aa） Fragment：G-domain Chain B 3–169（167 aa） Fragment：G-domain	Mutation：Y35A Mutation：Y35A	MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris hydrochloride, 200 mM Sodium acetate trihydrate, 30% w/v Polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.214
3T5G Structure of fully modified farnesylated Rheb in complex with PDE6D Deposited 2011-07-27	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 A 1–181（181 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 FAR FARNESYL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；0.1 M Tris 8.5, and 12.5 % PEG8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.235
6BCU Cryo-EM structure of the activated RHEB-mTORC1 refined to 3.4 angstrom Deposited 2017-10-20	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 × 10 PDB declaration: decameric	Chain R 1–184（184 aa） Chain S 1–184（184 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 6 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6BSX CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND 1 AT 1.65A RESOLUTION Deposited 2017-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa） Fragment：RHEB VCID 10367	Not recorded	MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 E7S (5,6-dimethyl-1H-benzimidazol-2-yl)methanol × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.8；293 K；28% PEG4000, 0.2M SODIUM ACETATE, 0.1M TRIS-HCL, PH 8.8, SITTING DROP, TEMPERATURE 293K	Resolution 1.65 Å R-free 0.244
6BSX CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND 1 AT 1.65A RESOLUTION Deposited 2017-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–169（169 aa） Fragment：RHEB VCID 10367	Not recorded	MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 E7S (5,6-dimethyl-1H-benzimidazol-2-yl)methanol × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.8；293 K；28% PEG4000, 0.2M SODIUM ACETATE, 0.1M TRIS-HCL, PH 8.8, SITTING DROP, TEMPERATURE 293K	Resolution 1.65 Å R-free 0.244
6BSX CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND 1 AT 1.65A RESOLUTION Deposited 2017-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–169（169 aa） Fragment：RHEB VCID 10367	Not recorded	MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 E7S (5,6-dimethyl-1H-benzimidazol-2-yl)methanol × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.8；293 K；28% PEG4000, 0.2M SODIUM ACETATE, 0.1M TRIS-HCL, PH 8.8, SITTING DROP, TEMPERATURE 293K	Resolution 1.65 Å R-free 0.244
6BSX CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND 1 AT 1.65A RESOLUTION Deposited 2017-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–169（169 aa） Fragment：RHEB VCID 10367	Not recorded	MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 E7S (5,6-dimethyl-1H-benzimidazol-2-yl)methanol × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.8；293 K；28% PEG4000, 0.2M SODIUM ACETATE, 0.1M TRIS-HCL, PH 8.8, SITTING DROP, TEMPERATURE 293K	Resolution 1.65 Å R-free 0.244
6BT0 CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND NR1 Deposited 2017-12-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；19% PEG 1500, 0.1M Na acetate pH 5.0	Resolution 2.60 Å R-free 0.316
6BT0 CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND NR1 Deposited 2017-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–169（169 aa）	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 E7V 4-bromo-6-[(3,4-dichlorophenyl)sulfanyl]-1-{[4-(dimethylcarbamoyl)phenyl]methyl}-1H-indole-2-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；19% PEG 1500, 0.1M Na acetate pH 5.0	Resolution 2.60 Å R-free 0.316
6BT0 CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND NR1 Deposited 2017-12-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–169（169 aa）	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；19% PEG 1500, 0.1M Na acetate pH 5.0	Resolution 2.60 Å R-free 0.316
6BT0 CRYSTAL STRUCTURE OF RHEB IN COMPLEX WITH COMPOUND NR1 Deposited 2017-12-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–169（169 aa）	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；19% PEG 1500, 0.1M Na acetate pH 5.0	Resolution 2.60 Å R-free 0.316
7BTA Crystal structure of Rheb D60K mutant bound to GDP Deposited 2020-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa） Fragment：GTPase domain	Mutation：D60K	GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；290 K；0.2 M NaH2PO4: 16% PEG 3350	Resolution 2.60 Å R-free 0.256
7BTA Crystal structure of Rheb D60K mutant bound to GDP Deposited 2020-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–169（169 aa） Fragment：GTPase domain	Mutation：D60K	GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；290 K；0.2 M NaH2PO4: 16% PEG 3350	Resolution 2.60 Å R-free 0.256
7BTC Crystal structure of Rheb Y35N mutant bound to GDP Deposited 2020-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa） Fragment：GTPase domain	Mutation：Y35N	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；290 K；0.10% n-Octyl-beta-D-glucoside: 0.1 M Sodium citrate tribasic, pH 5.5: 22% PEG 3350	Resolution 2.10 Å R-free 0.233
7BTC Crystal structure of Rheb Y35N mutant bound to GDP Deposited 2020-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–169（169 aa） Fragment：GTPase domain	Mutation：Y35N	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；290 K；0.10% n-Octyl-beta-D-glucoside: 0.1 M Sodium citrate tribasic, pH 5.5: 22% PEG 3350	Resolution 2.10 Å R-free 0.233
7BTC Crystal structure of Rheb Y35N mutant bound to GDP Deposited 2020-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–169（169 aa） Fragment：GTPase domain	Mutation：Y35N	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；290 K；0.10% n-Octyl-beta-D-glucoside: 0.1 M Sodium citrate tribasic, pH 5.5: 22% PEG 3350	Resolution 2.10 Å R-free 0.233
7BTC Crystal structure of Rheb Y35N mutant bound to GDP Deposited 2020-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–169（169 aa） Fragment：GTPase domain	Mutation：Y35N	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；290 K；0.10% n-Octyl-beta-D-glucoside: 0.1 M Sodium citrate tribasic, pH 5.5: 22% PEG 3350	Resolution 2.10 Å R-free 0.233
7BTD Crystal structure of Rheb Y35N mutant bound to GppNHp Deposited 2020-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa） Fragment：GTPase domain	Mutation：Y35N	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；290 K；0.2 M Ammonium acetate: 0.1 M HEPES, pH 7.5: 25% PEG 3350.	Resolution 2.00 Å R-free 0.208
9ED4 A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane Deposited 2024-11-15	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 × 24 PDB declaration: 24-meric	Chain L 1–184（184 aa） Chain N 1–184（184 aa）	Not recorded	GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 2 MG MAGNESIUM ION × 8 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 IHP INOSITOL HEXAKISPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
9ED7 Active state of mTOR on membrane Deposited 2024-11-16	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 L 1–184（184 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9ED8 Intermediate state of mTOR on membrane Deposited 2024-11-16	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 L 1–184（184 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.61 Å

14 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RHEB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–169； UniProt 2–169 Author chain B； PDBConstruct 2–169； UniProt 2–169 Author chain C； PDBConstruct 2–169； UniProt 2–169 Author chain D； PDBConstruct 2–169； UniProt 2–169

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	5yxh
Deposition date deposition_date	2017-12-05
Structure title title	Structure of Rheb-GDP
Keywords keywords	GTPase, mTORC1 signaling, Rheb, SIGNALING PROTEIN; SIGNALING PROTEIN
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	28.78 Å
Radius of gyration Rg (electron density) rg_electron	27.84 Å
Forward intensity I(0) i0	89150500.00
Molecular weight molecular_weight	75054.0 kDa
Excluded volume excluded_volume	94336 Å³
Envelope volume envelope_volume	118140 Å³
Hydration-shell volume shell_volume	35054 Å³
Envelope diameter envelope_diameter	94.4 Å
Shell Rg shell_rg	35.50 Å
Envelope Rg envelope_rg	27.60 Å
Shape Rg shape_rg	27.83 Å
Total Rg total_rg	28.66 Å
Total atoms total_atoms	5277
Residues n_residues	651
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	88.4 Å
Rg (real space) rg_real	28.65 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	8.9150e+07
I(0) uncertainty (real space) i0_real_error	1.2160e+06
Rg (reciprocal space) rg_reciprocal	28.71 Å
I(0) (reciprocal space) i0_reciprocal	89150000.0000
Solution quality estimate total_estimate	0.9100
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	86.8 Å
Skewness Skewness skewness	0.099
Kurtosis Kurtosis kurtosis	-0.599
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16960000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.968

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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	GTP-binding protein Rheb
Molecular weight formula_weight	19276.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5424

SPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKLE

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 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5yxha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d5yxha2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5yxhb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d5yxhb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5yxhc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d5yxhc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5yxhd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d5yxhd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	5yxhA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5yxhB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5yxhC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5yxhD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	50.166 Å
Unit-cell length b length_b	58.963 Å
Unit-cell length c length_c	64.345 Å
Unit-cell angle α angle_alpha	110.53 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	108.16 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.040 Å
Low-resolution limit resolution_low	59.800 Å
R factor r_factor	0.2464
R_work r_work	0.2438
R_free r_free	0.2986

fit	/app/data/saxs_computation/yx/5yxh/5yxh.fit
pddf	/app/data/pr_computation/yx/5yxh/5yxh.pr.out
profile	/app/data/saxs_computation/yx/5yxh/5yxh.dat

Structure of Rheb-GDP

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

GTP-binding protein Rheb

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