SAXSdb — 9wbd

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1. Structure Basics

entry_id	9wbd
deposition_date	2025-08-13
title	Crystal structure of HLA-B*07:02 in complex with SPR epitope and Q04 TCR
keywords	pMHC-TCR complex, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	50.42 Å
rg_electron	49.94 Å
i0	1954420000.00
molecular_weight	358520.0 kDa
excluded_volume	443220 Å³
envelope_volume	643040 Å³
shell_volume	104930 Å³
envelope_diameter	175.2 Å
shell_rg	56.00 Å
envelope_rg	48.73 Å
shape_rg	49.92 Å
total_rg	50.18 Å
total_atoms	25351
n_residues	3238
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

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3. P(r) Analysis (GNOM)

dmax	162.7 Å
rg_real	50.22 Å
rg_real_error	1.36 Å
i0_real	1.9540e+09
i0_real_error	3.4440e+07
rg_reciprocal	50.57 Å
i0_reciprocal	1955000000.0000
total_estimate	0.8088
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	68.2 Å
skewness	0.163
kurtosis	-0.316
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	139800000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	T cell receptor alpha variable 25,T cell receptor alpha chain constant
formula_weight	23105.7 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,F,K,P
atom_count	25365

MGQQVMQIPQYQHVQEGEDFTTYCNSSTTLSNIQWYKQRPGGHPVFLIQLVKSGEVKKQKRLTFQFGEAKKNSSLHITATQTTDVGTYFCAGYTSGTYKYIFGTGTRLKVLANIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	TCR beta
formula_weight	27205.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,G,L,Q

MGAGVSQSPRYKVAKRGQDVALRCDPISGHVSLFWYQQALGQGPEFLTYFQNEAQLDKSGLPSDRFFAERPEGSVSTLKIQRTQQEDSAVYLCASSLGQGHFTFGSGTRLTVVEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	HLA class I histocompatibility antigen, B alpha chain
formula_weight	32093.2 kDa
src_method	man
entity_count	4

Polymer

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

MGSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHDQYAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGECVEWLRRYLENGKDKLERADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	Beta-2-microglobulin
formula_weight	11879.4 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	D,I,N,S

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

description	Nucleoprotein
formula_weight	1295.5 kDa
src_method	syn
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,J,O,T

SPRWYFYYL

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	14

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6. Citations (1)

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length_a	88.786 Å
length_b	102.564 Å
length_c	120.701 Å
angle_alpha	84.14 °
angle_beta	68.60 °
angle_gamma	81.10 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.750 Å
resolution_low	48.520 Å
r_factor	0.2205
r_work	0.2179
r_free	0.2700

fit	/app/data/saxs_computation/wb/9wbd/9wbd.fit
pddf	/app/data/pr_computation/wb/9wbd/9wbd.pr.out
profile	/app/data/saxs_computation/wb/9wbd/9wbd.dat

Crystal structure of HLA-B*07:02 in complex with SPR epitope and Q04 TCR

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)