SAXSdb — 9y0w

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1. Structure Basics

entry_id	9y0w
deposition_date	2025-08-29
title	Crystal Structure of human MAIT A-F7 TCR-MR1*05-5-OP-RU complex
keywords	MAIT TCR, MR1, metabolite presentation, 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	49.46 Å
rg_electron	49.73 Å
i0	480329000.00
molecular_weight	180130.0 kDa
excluded_volume	224150 Å³
envelope_volume	317580 Å³
shell_volume	55036 Å³
envelope_diameter	178.3 Å
shell_rg	50.59 Å
envelope_rg	49.78 Å
shape_rg	49.74 Å
total_rg	49.73 Å
total_atoms	12721
n_residues	1608
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	161.9 Å
rg_real	49.82 Å
rg_real_error	2.02 Å
i0_real	4.8030e+08
i0_real_error	9.3220e+06
rg_reciprocal	49.47 Å
i0_reciprocal	480100000.0000
total_estimate	0.8057
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	40.5 Å
skewness	0.346
kurtosis	-0.647
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	34490000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Major histocompatibility complex class I-related protein 1
formula_weight	31615.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	13748

MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAGNLAPDHWERYTQLLRGWQQMFKVELKRLQRHYNHSGSQTYQRMIGCELLEDGSTTGFLQYAYDGQDFLIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRTEPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQAWASVELDPQSSNLYSCHVEHSGVHMVLQVP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	B,F

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	TCR alpha chain
formula_weight	22781.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,G

MGQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFSSFLSRSKGYSYLLLKELQMKDSASYLCAVKDSNYQLIWGAGTKLIIKPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	TCR beta chain
formula_weight	27677.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,H

MNAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSVWTGEGSGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 non-polymer

description	1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol
formula_weight	330.3 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	771

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6. Citations (1)

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length_a	213.432 Å
length_b	69.501 Å
length_c	143.205 Å
angle_alpha	90.00 °
angle_beta	103.94 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.400 Å
resolution_low	48.980 Å
r_factor	0.1803
r_work	0.1794
r_free	0.2170

fit	/app/data/saxs_computation/y0/9y0w/9y0w.fit
pddf	/app/data/pr_computation/y0/9y0w/9y0w.pr.out
profile	/app/data/saxs_computation/y0/9y0w/9y0w.dat

Crystal Structure of human MAIT A-F7 TCR-MR1*05-5-OP-RU complex

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 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)