← Back to search

9qwk

Crystal structure of S2c-a5b6 TCR in complex with CD1c

Method: X-RAY DIFFRACTION D_max: 219.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qwk
deposition_date	2025-04-14
last_revision	2025-08-20
title	Crystal structure of S2c-a5b6 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	64.53 Å
rg_electron	65.11 Å
i0	1967830000.00
molecular_weight	369550.0 kDa
excluded_volume	460330 Å³
envelope_volume	727440 Å³
shell_volume	99562 Å³
envelope_diameter	252.7 Å
shell_rg	60.81 Å
envelope_rg	63.49 Å
shape_rg	65.08 Å
total_rg	65.12 Å
total_atoms	26095
n_residues	3226
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	219.3 Å
rg_real	64.99 Å
rg_real_error	1.65 Å
i0_real	1.9650e+09
i0_real_error	4.1700e+07
rg_reciprocal	63.84 Å
i0_reciprocal	1963000000.0000
total_estimate	0.8460
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	73.1 Å
skewness	0.602
kurtosis	0.076
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0080
highest_alpha	94460000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.494

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (12)

Entity 1 polymer

description	Beta-2-microglobulin,T-cell surface glycoprotein CD1c
formula_weight	49744.5 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,G,J,L,O,Q,T
atom_count	26177

MYRMQLLSCIALSLALVTNSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDIGGGGSGGGGSGGGGSEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHNWSKGNFSNEELSDLELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGKSPEGFFQVAFNGLDLLSFQNTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDAGKMYVHRQVRPEAWLSSRPSLGSGQLLLVCHASGFYPKPVWVTWMRNEQEQLGTKHGDILPNADGTWYLQVILEVASEEPAGLSCRVRHSSLGGQDIILYWGSLSTPPTPSTPPTGLNDIFEAQKIEWHEHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	TCR alpha
formula_weight	22099.5 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	D,H,M,R

MGNSVTQMEGPVTLSEEAFLTINCTYTAYGLYSLFWYVQYPGEGLQLLLKATKADDKGSNKGFEATYRKETTSFHLEKGSVQVSDSAVYFCALSGQYGWGKLQFGAGTQVVVTPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTQVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSQKSDFACANAFQNSIIPEDT

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	TCR beta
formula_weight	28118.3 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,F,K,P

MDTGVSQNPRHKITKRGQNVTFRCDPISEHSRLYWYRQTLGQGPEFLTYFQNEAQLEKSRLLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSPRMVRGAEAFFGQGTRLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALQDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 branched

description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	367.3 kDa
src_method	man
entity_count	2

Entity 5 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	383.3 kDa
src_method	man
entity_count	1

Entity 6 branched

description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	732.7 kDa
src_method	man
entity_count	1

Entity 7 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	2

Entity 8 non-polymer

description	DECANE
formula_weight	142.3 kDa
src_method	syn
entity_count	8

Entity 9 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 10 non-polymer

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

Entity 11 non-polymer

description	alpha-L-fucopyranose
formula_weight	164.2 kDa
src_method	syn
entity_count	1

Entity 12 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	82

▶

6. Citations (1)

▶

length_a	82.233 Å
length_b	83.652 Å
length_c	180.130 Å
angle_alpha	91.85 °
angle_beta	95.99 °
angle_gamma	115.61 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.270 Å
resolution_low	89.240 Å
r_factor	0.2265
r_work	0.2263
r_free	0.2529

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

Crystal structure of S2c-a5b6 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 (12)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 branched

Entity 6 branched

Entity 7 branched

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)