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5dj4

Leucine-bound Sestrin2 from Homo sapiens

Method: X-RAY DIFFRACTION Dmax: 157.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sestrin-2

Homo sapiens

UniProt P58004

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 1–480 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–480 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–480 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 1–480 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
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain E； UniProt 1–480 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
6 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–480 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
7 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–480 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
8 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 1–480 Chain D； UniProt 1–480 Chain E； UniProt 1–480 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

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 5DJ4 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 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 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 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 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 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
5T0N Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution Deposited 2016-08-16 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 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 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 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 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
6N0M CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138 Deposited 2018-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 66–480（415 aa）
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
6N0M CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138 Deposited 2018-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 66–480（415 aa）
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
6N0M CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138 Deposited 2018-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 66–480（415 aa）
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
6N0M CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138 Deposited 2018-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 66–480（415 aa）
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
6N0M CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138 Deposited 2018-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 66–480（415 aa）
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
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 17 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 1–480； UniProt 1–480 Author chain B； PDBConstruct 1–480； UniProt 1–480 Author chain C； PDBConstruct 1–480； UniProt 1–480 Author chain D； PDBConstruct 1–480； UniProt 1–480 Author chain E； PDBConstruct 1–480； UniProt 1–480

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5dj4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5dj4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5dj4
Deposition date deposition_date2015-09-01
Structure title titleLeucine-bound Sestrin2 from Homo sapiens
Keywords keywordsmTOR, leucine, amino-acid, sensing, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier48.24 Å
Radius of gyration Rg (electron density) rg_electron48.22 Å
Forward intensity I(0) i0621953000.00
Molecular weight molecular_weight209840.0 kDa
Excluded volume excluded_volume263150 ų
Envelope volume envelope_volume357310 ų
Hydration-shell volume shell_volume61168 ų
Envelope diameter envelope_diameter147.7 Å
Shell Rg shell_rg53.66 Å
Envelope Rg envelope_rg46.70 Å
Shape Rg shape_rg48.23 Å
Total Rg total_rg48.37 Å
Total atoms total_atoms14796
Residues n_residues1824
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax157.2 Å
Rg (real space) rg_real48.14 Å
Rg uncertainty (real space) rg_real_error1.46 Å
I(0) (real space) i0_real6.2200e+08
I(0) uncertainty (real space) i0_real_error1.2920e+07
Rg (reciprocal space) rg_reciprocal48.24 Å
I(0) (reciprocal space) i0_reciprocal622000000.0000
Solution quality estimate total_estimate0.8912
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary66.7 Å
Skewness Skewness skewness0.129
Kurtosis Kurtosis kurtosis-0.674
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha82580000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.910
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)