SAXSdb — 1i9e

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

CYTOTOXIC TCELL VALPHA DOMAIN

Mus musculus

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 21–135	Fragment：N-TERMINAL DOMAIN OF ALPHA CHAIN	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；295 K；di-sodium tartrate, NaCl, imidazole/HCl, pH 7.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.50 Å R-free 0.233

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 1I9E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1G6R A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST TCR/MHC COMPLEX Deposited 2000-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 21–130（110 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；295 K；0.2 M Tris/acetate, 10% PEG 6000, pH 7.2, VAPOR DIFFUSION, temperature 22K	Resolution 2.80 Å R-free 0.327
1G6R A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST TCR/MHC COMPLEX Deposited 2000-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 21–130（110 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；295 K；0.2 M Tris/acetate, 10% PEG 6000, pH 7.2, VAPOR DIFFUSION, temperature 22K	Resolution 2.80 Å R-free 0.327
2ICW Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule Deposited 2006-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 21–130（110 aa） Fragment：residues 21-131	Mutation：W82R, L43P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.6；298 K；13-15% PEG 4000, 5% isopropanol, 0.1 M sodium citrate, 2 mM zinc acetate, pH 5.6, EVAPORATION, temperature 298K	Resolution 2.41 Å R-free 0.288
2ICW Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule Deposited 2006-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain K 21–130（110 aa） Fragment：residues 21-131	Mutation：W82R, L43P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.6；298 K；13-15% PEG 4000, 5% isopropanol, 0.1 M sodium citrate, 2 mM zinc acetate, pH 5.6, EVAPORATION, temperature 298K	Resolution 2.41 Å R-free 0.288
2OI9 Structure of the 2C/Ld/QL9 allogeneic complex Deposited 2007-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 21–130（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；0.9M sodium dihydrogen phosphate, 0.01M di-potassium hydrogen phosphate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.35 Å R-free 0.226
3E2H Structure of the m67 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 22–130（109 aa）	Mutation：L43P, W82R, G99L, F100E, A101R, S102P, A103Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；2M ammonium tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.80 Å R-free 0.276
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 22–130（109 aa）	Mutation：L43P, W82R, G99D F100P A101P S102P A103L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 22–130（109 aa）	Mutation：L43P, W82R, G99D F100P A101P S102P A103L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain d 22–130（109 aa）	Mutation：L43P, W82R, G99D F100P A101P S102P A103L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 22–130（109 aa）	Mutation：L43P, W82R, G99D F100P A101P S102P A103L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain M 22–130（109 aa）	Mutation：L43P, W82R, G99D F100P A101P S102P A103L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 22–130（109 aa）	Mutation：L43P, W82R, G99D F100P A101P S102P A103L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 22–130（109 aa）	Mutation：L43P, W82R, G99D F100P A101P S102P A103L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Z 22–130（109 aa）	Mutation：L43P, W82R, G99D F100P A101P S102P A103L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275

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

View Construct and Data Evidence

UniProt name	TVA1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–115； UniProt 21–135

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	1i9e
Deposition date deposition_date	2001-03-19
Structure title title	TCR DOMAIN
Keywords keywords	Ig-like domain, T Cell receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
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	15.71 Å
Radius of gyration Rg (electron density) rg_electron	14.60 Å
Forward intensity I(0) i0	3241900.00
Molecular weight molecular_weight	12971.0 kDa
Excluded volume excluded_volume	16360 Å³
Envelope volume envelope_volume	18597 Å³
Hydration-shell volume shell_volume	11365 Å³
Envelope diameter envelope_diameter	62.0 Å
Shell Rg shell_rg	20.01 Å
Envelope Rg envelope_rg	15.34 Å
Shape Rg shape_rg	14.59 Å
Total Rg total_rg	15.81 Å
Total atoms total_atoms	919
Residues n_residues	115
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	63.1 Å
Rg (real space) rg_real	15.78 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	3.2420e+06
I(0) uncertainty (real space) i0_real_error	4.2360e+04
Rg (reciprocal space) rg_reciprocal	15.77 Å
I(0) (reciprocal space) i0_reciprocal	3242000.0000
Solution quality estimate total_estimate	0.7512
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.606
Kurtosis Kurtosis kurtosis	0.521
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	887300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.385; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.608; Smooth: 0.999

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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	CYTOTOXIC TCELL VALPHA DOMAIN
Molecular weight formula_weight	12774.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	963

QSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQLLLKYYSGDPVVQGVNGFEAEFSKSNSSFHLRKASVHWSDSAVYFCAVSGFASALTFGSGTKVIVLPYIQN

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Drosophila melanogaster

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
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	44

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1i9ea_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (1 domains)

Domain ID domain_id	1i9eA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	104.032 Å
Unit-cell length b length_b	104.032 Å
Unit-cell length c length_c	63.090 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	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	37.500 Å
R factor r_factor	0.2063
R_work r_work	0.2031
R_free r_free	0.2328

fit	/app/data/saxs_computation/i9/1i9e/1i9e.fit
pddf	/app/data/pr_computation/i9/1i9e/1i9e.pr.out
profile	/app/data/saxs_computation/i9/1i9e/1i9e.dat

TCR DOMAIN

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

CYTOTOXIC TCELL VALPHA DOMAIN

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