SAXSdb — 6n0m

▼

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

Sestrin-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 66–480	Not recorded	K94 4-(difluoromethyl)-L-leucine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；1.35M Na malonate pH 6.5, 0.1M Mes pH 6.0	Resolution 3.30 Å R-free 0.250
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 66–480	Not recorded	K94 4-(difluoromethyl)-L-leucine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；1.35M Na malonate pH 6.5, 0.1M Mes pH 6.0	Resolution 3.30 Å R-free 0.250
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 66–480	Not recorded	K94 4-(difluoromethyl)-L-leucine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；1.35M Na malonate pH 6.5, 0.1M Mes pH 6.0	Resolution 3.30 Å R-free 0.250
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 66–480	Not recorded	K94 4-(difluoromethyl)-L-leucine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；1.35M Na malonate pH 6.5, 0.1M Mes pH 6.0	Resolution 3.30 Å R-free 0.250
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 66–480	Not recorded	K94 4-(difluoromethyl)-L-leucine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；1.35M Na malonate pH 6.5, 0.1M Mes pH 6.0	Resolution 3.30 Å R-free 0.250

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 6N0M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CUF X-ray crystal structure of SeMet human Sestrin2 Deposited 2015-07-24	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 1–480（480 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M MES 1.15 M sodium malonate	Resolution 3.50 Å R-free 0.272
5CUF X-ray crystal structure of SeMet human Sestrin2 Deposited 2015-07-24	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 1–480（480 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M MES 1.15 M sodium malonate	Resolution 3.50 Å R-free 0.272
5CUF X-ray crystal structure of SeMet human Sestrin2 Deposited 2015-07-24	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 1–480（480 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M MES 1.15 M sodium malonate	Resolution 3.50 Å R-free 0.272
5CUF X-ray crystal structure of SeMet human Sestrin2 Deposited 2015-07-24	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 1–480（480 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M MES 1.15 M sodium malonate	Resolution 3.50 Å R-free 0.272
5CUF X-ray crystal structure of SeMet human Sestrin2 Deposited 2015-07-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–480（480 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M MES 1.15 M sodium malonate	Resolution 3.50 Å R-free 0.272
5DJ4 Leucine-bound Sestrin2 from Homo sapiens Deposited 2015-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.2 M disodium malonate, 0.1 M MES pH 6.0, 1% (v/v) Jeffamine ED 2001	Resolution 2.70 Å R-free 0.223
5DJ4 Leucine-bound Sestrin2 from Homo sapiens Deposited 2015-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.2 M disodium malonate, 0.1 M MES pH 6.0, 1% (v/v) Jeffamine ED 2001	Resolution 2.70 Å R-free 0.223
5DJ4 Leucine-bound Sestrin2 from Homo sapiens Deposited 2015-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.2 M disodium malonate, 0.1 M MES pH 6.0, 1% (v/v) Jeffamine ED 2001	Resolution 2.70 Å R-free 0.223
5DJ4 Leucine-bound Sestrin2 from Homo sapiens Deposited 2015-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.2 M disodium malonate, 0.1 M MES pH 6.0, 1% (v/v) Jeffamine ED 2001	Resolution 2.70 Å R-free 0.223
5DJ4 Leucine-bound Sestrin2 from Homo sapiens Deposited 2015-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.2 M disodium malonate, 0.1 M MES pH 6.0, 1% (v/v) Jeffamine ED 2001	Resolution 2.70 Å R-free 0.223
5DJ4 Leucine-bound Sestrin2 from Homo sapiens Deposited 2015-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–480（480 aa）	Not recorded	LEU LEUCINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.2 M disodium malonate, 0.1 M MES pH 6.0, 1% (v/v) Jeffamine ED 2001	Resolution 2.70 Å R-free 0.223
5DJ4 Leucine-bound Sestrin2 from Homo sapiens Deposited 2015-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 1–480（480 aa）	Not recorded	LEU LEUCINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.2 M disodium malonate, 0.1 M MES pH 6.0, 1% (v/v) Jeffamine ED 2001	Resolution 2.70 Å R-free 0.223
5DJ4 Leucine-bound Sestrin2 from Homo sapiens Deposited 2015-09-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 1–480（480 aa） Chain D 1–480（480 aa） Chain E 1–480（480 aa）	Not recorded	LEU LEUCINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.2 M disodium malonate, 0.1 M MES pH 6.0, 1% (v/v) Jeffamine ED 2001	Resolution 2.70 Å R-free 0.223
5T0N Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution Deposited 2016-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；0.1 M MES pH 6.0, 1.2 M sodium malonate, 1% (w/v) Jeffamine ED 2001	Resolution 3.00 Å R-free 0.225
5T0N Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution Deposited 2016-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；0.1 M MES pH 6.0, 1.2 M sodium malonate, 1% (w/v) Jeffamine ED 2001	Resolution 3.00 Å R-free 0.225
5T0N Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution Deposited 2016-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；0.1 M MES pH 6.0, 1.2 M sodium malonate, 1% (w/v) Jeffamine ED 2001	Resolution 3.00 Å R-free 0.225
5T0N Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution Deposited 2016-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；0.1 M MES pH 6.0, 1.2 M sodium malonate, 1% (w/v) Jeffamine ED 2001	Resolution 3.00 Å R-free 0.225
5T0N Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution Deposited 2016-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–480（480 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；0.1 M MES pH 6.0, 1.2 M sodium malonate, 1% (w/v) Jeffamine ED 2001	Resolution 3.00 Å R-free 0.225
9LVJ Cryo-EM structure of Sestrin2 bound human GATOR2 complex Deposited 2025-02-12	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 × 18 PDB declaration: octadecameric	Chain U 1–480（480 aa） Chain V 1–480（480 aa）	Not recorded	ZN ZINC ION × 32	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
9LWF Cryo-EM structure of dual sensor bound GATOR2 complex Deposited 2025-02-14	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 × 20 PDB declaration: eicosameric	Chain X 1–480（480 aa） Chain Y 1–480（480 aa）	Mutation：Y375F Mutation：Y375F	ZN ZINC ION × 32	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å

5 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SESN2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–415； UniProt 66–480 Author chain B； PDBConstruct 1–415； UniProt 66–480 Author chain C； PDBConstruct 1–415； UniProt 66–480 Author chain D； PDBConstruct 1–415； UniProt 66–480 Author chain E； PDBConstruct 1–415； UniProt 66–480

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	6n0m
Deposition date deposition_date	2018-11-07
Structure title title	CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138
Keywords keywords	MTOR, LEUCINE, AMINO-ACID, SENSING, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	47.88 Å
Radius of gyration Rg (electron density) rg_electron	47.87 Å
Forward intensity I(0) i0	624147000.00
Molecular weight molecular_weight	210090.0 kDa
Excluded volume excluded_volume	263360 Å³
Envelope volume envelope_volume	350230 Å³
Hydration-shell volume shell_volume	60338 Å³
Envelope diameter envelope_diameter	146.6 Å
Shell Rg shell_rg	53.36 Å
Envelope Rg envelope_rg	46.49 Å
Shape Rg shape_rg	47.88 Å
Total Rg total_rg	48.02 Å
Total atoms total_atoms	14811
Residues n_residues	1824
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	152.2 Å
Rg (real space) rg_real	47.78 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	6.2410e+08
I(0) uncertainty (real space) i0_real_error	9.6120e+06
Rg (reciprocal space) rg_reciprocal	47.88 Å
I(0) (reciprocal space) i0_reciprocal	624200000.0000
Solution quality estimate total_estimate	0.8281
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	64.6 Å
Skewness Skewness skewness	0.127
Kurtosis Kurtosis kurtosis	-0.677
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	67290000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Sestrin-2
Molecular weight formula_weight	47458.7 kDa
EC 编号 ec_number	1.11.1.15
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	14811

GLEALMSSGRVDNLAVVMGLHPDYFTSFWRLHYLLLHTDGPLASSWRHYIAIMAAARHQCSYLVGSHMAEFLQTGGDPEWLLGLHRAPEKLRKLSEINKLLAHRPWLITKEHIQALLKTGEHTWSLAELIQALVLLTHCHSLSSFVFGCGILPEGDADGSPAPQAPTPPSEQSSPPSRDPLNNSGGFESARDVEALMERMQQLQESLLRDEGTSQEEMESRFELEKSESLLVTPSADILEPSPHPDMLCFVEDPTFGYEDFTRRGAQAPPTFRAQDYTWEDHGYSLIQRLYPEGGQLLDEKFQAAYSLTYNTIAMHSGVDTSVLRRAIWNYIHCVFGIRYDDYDYGEVNQLLERNLKVYIKTVACYPEKTTRRMYNLFWRHFRHSEKVHVNLLLLEARMQAALLYALRAITRYMT

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 non-polymer

Description description	4-(difluoromethyl)-L-leucine
Molecular weight formula_weight	181.2 kDa
Source method src_method	syn
Copy count entity_count	5

▶

8. Citations (1)

▶

Unit-cell length a length_a	290.410 Å
Unit-cell length b length_b	290.410 Å
Unit-cell length c length_c	290.410 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	120

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	48.400 Å
R factor r_factor	0.1869
R_work r_work	0.1836
R_free r_free	0.2502

fit	/app/data/saxs_computation/n0/6n0m/6n0m.fit
pddf	/app/data/pr_computation/n0/6n0m/6n0m.pr.out
profile	/app/data/saxs_computation/n0/6n0m/6n0m.dat

CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138

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

Sestrin-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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)