9dl0

Crystal structure of a synthetic Fab (R3H8) in complex with the FRB domain of mTOR

Method: X-RAY DIFFRACTION Dmax: 110.5 Å Quality: EXCELLENT

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

Serine/threonine-protein kinase mTOR

Homo sapiens

UniProt P42345

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 2021–2113 Not recorded Fab heavy chain × 1 Fab light chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1 M HEPES pH 7.5 4% PEG 400 2.2 M ammonium sulfate Resolution 2.00 Å R-free 0.234
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain I; UniProt 2021–2113 Not recorded Fab heavy chain × 1 Fab light chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;0.1 M HEPES pH 7.5 4% PEG 400 2.2 M ammonium sulfate Resolution 2.00 Å R-free 0.234

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.

66 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MTOR_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain G; PDBConstruct 2–94; UniProt 2021–2113 Author chain I; PDBConstruct 2–94; UniProt 2021–2113

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 9dl0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dl0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9dl0
Deposition date deposition_date2024-09-10
Structure title titleCrystal structure of a synthetic Fab (R3H8) in complex with the FRB domain of mTOR
Keywords keywordskinase, inhibitor, antibody, signaling protein, IMMUNE SYSTEM, IMMUNE SYSTEM-Transferase complex; IMMUNE SYSTEM/Transferase
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.76
Radius of gyration Rg (electron density) rg_electron34.04
Forward intensity I(0) i0211219000.00
Molecular weight molecular_weight115190.0 kDa
Excluded volume excluded_volume143490 ų
Envelope volume envelope_volume190360 ų
Hydration-shell volume shell_volume46345 ų
Envelope diameter envelope_diameter117.8
Shell Rg shell_rg41.10
Envelope Rg envelope_rg33.40
Shape Rg shape_rg34.00
Total Rg total_rg34.71
Total atoms total_atoms8464
Residues n_residues1056
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.5
Rg (real space) rg_real34.64
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real2.1120e+08
I(0) uncertainty (real space) i0_real_error3.2130e+06
Rg (reciprocal space) rg_reciprocal34.72
I(0) (reciprocal space) i0_reciprocal211200000.0000
Solution quality estimate total_estimate0.9018
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.6
Skewness Skewness skewness0.181
Kurtosis Kurtosis kurtosis-0.447
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha20970000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.945

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)