← Back to search

9qwj

Crystal structure of S2c TCR in complex with CD1c

Method: X-RAY DIFFRACTION D_max: 184.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qwj
deposition_date	2025-04-14
last_revision	2025-08-20
title	Crystal structure of S2c TCR in complex with CD1c
keywords	T cell receptor, TCR, CD1c, lipids, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	53.10 Å
rg_electron	53.26 Å
i0	512206000.00
molecular_weight	184960.0 kDa
excluded_volume	230290 Å³
envelope_volume	341500 Å³
shell_volume	59161 Å³
envelope_diameter	195.0 Å
shell_rg	48.62 Å
envelope_rg	52.84 Å
shape_rg	53.21 Å
total_rg	53.24 Å
total_atoms	13055
n_residues	1604
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	184.7 Å
rg_real	53.63 Å
rg_real_error	2.23 Å
i0_real	5.1220e+08
i0_real_error	1.1260e+07
rg_reciprocal	52.65 Å
i0_reciprocal	511500000.0000
total_estimate	0.8075
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.4 Å
skewness	0.607
kurtosis	-0.066
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	25320000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.246

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (11)

Entity 1 polymer

description	Beta-2-microglobulin,T-cell surface glycoprotein CD1c
formula_weight	49744.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,N
atom_count	13571

MYRMQLLSCIALSLALVTNSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDIGGGGSGGGGSGGGGSEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHNWSKGNFSNEELSDLELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGKSPEGFFQVAFNGLDLLSFQNTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDAGKMYVHRQVRPEAWLSSRPSLGSGQLLLVCHASGFYPKPVWVTWMRNEQEQLGTKHGDILPNADGTWYLQVILEVASEEPAGLSCRVRHSSLGGQDIILYWGSLSTPPTPSTPPTGLNDIFEAQKIEWHEHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	TCR alpha
formula_weight	21936.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,T

MGNSVTQMEGPVTLSEEAFLTINCTYTATGYPSLFWYVQYPGEGLQLLLKATKADDKGSNKGFEATYRKETTSFHLEKGSVQVSDSAVYFCALSDQYGWGKLQFGAGTQVVVTPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPED

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	TCR beta
formula_weight	28059.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,U

MDTGVSQNPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSRLLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSPRTGRGAEAFFGQGTRLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	7

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	6

Entity 7 non-polymer

description	beta-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	DODECANE
formula_weight	170.3 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

Entity 10 non-polymer

description	DECANE
formula_weight	142.3 kDa
src_method	syn
entity_count	2

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	511

▶

6. Citations (1)

▶

length_a	85.373 Å
length_b	122.068 Å
length_c	108.696 Å
angle_alpha	90.00 °
angle_beta	110.03 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.040 Å
resolution_low	67.030 Å
r_factor	0.2021
r_work	0.2004
r_free	0.2350

fit	/app/data/saxs_computation/qw/9qwj/9qwj.fit
pddf	/app/data/pr_computation/qw/9qwj/9qwj.pr.out
profile	/app/data/saxs_computation/qw/9qwj/9qwj.dat

Crystal structure of S2c TCR in complex with CD1c

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)