SAXSdb — 1d9k

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1. Structure Basics

entry_id	1d9k
deposition_date	1999-10-28
title	CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA
keywords	T-CELL RECEPTOR, MHC CLASS II, D10, I-AK, 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	48.72 Å
rg_electron	49.33 Å
i0	296260000.00
molecular_weight	140950.0 kDa
excluded_volume	175490 Å³
envelope_volume	247190 Å³
shell_volume	43866 Å³
envelope_diameter	168.6 Å
shell_rg	49.76 Å
envelope_rg	48.76 Å
shape_rg	49.28 Å
total_rg	49.51 Å
total_atoms	9962
n_residues	1218
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	158.2 Å
rg_real	49.37 Å
rg_real_error	1.79 Å
i0_real	2.9630e+08
i0_real_error	5.9150e+06
rg_reciprocal	48.72 Å
i0_reciprocal	296000000.0000
total_estimate	0.7601
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.6 Å
skewness	0.425
kurtosis	-0.697
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	16940000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.725; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.609; Smooth: 0.094

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	T-CELL RECEPTOR D10 (ALPHA CHAIN)
formula_weight	12399.9 kDa
mutation	C115S
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	9962

QVRQSPQSLTVWEGETTILNCSYEDSTFDYFPWYRQFPGKSPALLIAISLVSNKKEDGRFTIFFNKREKKLSLHITDSQPGDSATYFCAATGSFNKLTFGAGTRLAVSPY

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 polymer

description	T-CELL RECEPTOR D10 (BETA CHAIN)
formula_weight	12131.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGGQGRAEQFFGPGTRLTVLGS

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 3 polymer

description	MHC I-AK A CHAIN (ALPHA CHAIN)
formula_weight	20971.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

IEADHVGSYGITVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFAQLRRFEPQGGLQNIATGKHNLEILTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEI

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Cricetulus griseus

Entity 4 polymer

description	MHC I-AK B CHAIN (BETA CHAIN)
formula_weight	22340.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

GSERHFVHQFQPFCYFTNGTQRIRLVIRYIYNREEYVRFDSDVGEYRAVTELGRPDAEYWNKQYLERTRAELDTVCRHNYEKTETPTSLRRLEQPSVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Cricetulus griseus

Entity 5 polymer

description	CONALBUMIN PEPTIDE
formula_weight	1700.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	P,Q

GNSHRGAIEWEGIESG

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Cricetulus griseus

Entity 6 branched

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

Entity 7 non-polymer

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

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6. Citations (1)

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length_a	97.600 Å
length_b	345.300 Å
length_c	97.700 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	3.200 Å
resolution_low	15.000 Å
r_factor	0.0700
r_work	0.2470
r_free	0.2930

fit	/app/data/saxs_computation/d9/1d9k/1d9k.fit
pddf	/app/data/pr_computation/d9/1d9k/1d9k.pr.out
profile	/app/data/saxs_computation/d9/1d9k/1d9k.dat

CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 branched

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)