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9sko

Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS

Method: X-RAY DIFFRACTION D_max: 75.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sko
deposition_date	2025-09-02
title	Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS
keywords	HLA class I, Human leukocyte antigen class I, MHC class I, Major histocompatibility complex class I, 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	24.08 Å
rg_electron	22.98 Å
i0	38554200.00
molecular_weight	46351.0 kDa
excluded_volume	57179 Å³
envelope_volume	69348 Å³
shell_volume	25225 Å³
envelope_diameter	78.9 Å
shell_rg	29.82 Å
envelope_rg	23.14 Å
shape_rg	22.96 Å
total_rg	23.83 Å
total_atoms	3366
n_residues	383
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	75.8 Å
rg_real	24.02 Å
rg_real_error	0.49 Å
i0_real	3.8550e+07
i0_real_error	5.1620e+05
rg_reciprocal	24.03 Å
i0_reciprocal	38550000.0000
total_estimate	0.9082
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.6 Å
skewness	0.262
kurtosis	-0.443
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	10780000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	MHC class I antigen
formula_weight	31985.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3646

MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Source

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

Entity 2 polymer

description	Beta-2-microglobulin
formula_weight	11879.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

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

Entity 3 polymer

description	LLWNGPMAVS peptide
formula_weight	1087.3 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

LLWNGPMAVS

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	11

Entity 7 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	10

Entity 8 non-polymer

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

Entity 9 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	250

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6. Citations (1)

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length_a	59.928 Å
length_b	79.197 Å
length_c	111.400 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.490 Å
resolution_low	19.660 Å
r_factor	0.1853
r_work	0.1844
r_free	0.2041

fit	/app/data/saxs_computation/sk/9sko/9sko.fit
pddf	/app/data/pr_computation/sk/9sko/9sko.pr.out
profile	/app/data/saxs_computation/sk/9sko/9sko.dat

Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS

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 (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)