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1agd

ANTAGONIST HIV-1 GAG PEPTIDES INDUCE STRUCTURAL CHANGES IN HLA B8-HIV-1 GAG PEPTIDE (GGKKKYKL-INDEX PEPTIDE)

Method: X-RAY DIFFRACTION D_max: 75.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1agd
deposition_date	1997-03-24
title	ANTAGONIST HIV-1 GAG PEPTIDES INDUCE STRUCTURAL CHANGES IN HLA B8-HIV-1 GAG PEPTIDE (GGKKKYKL-INDEX PEPTIDE)
keywords	HLA B8, HIV, MHC CLASS I, HISTOCOMPATIBILITY COMPLEX; HISTOCOMPATIBILITY COMPLEX
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	24.05 Å
rg_electron	22.94 Å
i0	36494500.00
molecular_weight	44528.0 kDa
excluded_volume	54806 Å³
envelope_volume	67195 Å³
shell_volume	24531 Å³
envelope_diameter	79.3 Å
shell_rg	29.80 Å
envelope_rg	23.04 Å
shape_rg	22.92 Å
total_rg	23.80 Å
total_atoms	3146
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	75.2 Å
rg_real	23.98 Å
rg_real_error	0.50 Å
i0_real	3.6490e+07
i0_real_error	5.5060e+05
rg_reciprocal	24.00 Å
i0_reciprocal	36490000.0000
total_estimate	0.9107
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.4 Å
skewness	0.243
kurtosis	-0.484
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	8611000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	B*0801
formula_weight	31928.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3545

GSHSMRYFDTAMSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQIFKTNTQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHNQYAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAARVAEQDRAYLEGTCVEWLRRYLENGKDTLERADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	BETA-2 MICROGLOBULIN
formula_weight	11748.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	HIV-1 GAG PEPTIDE (GGKKKYKL - INDEX PEPTIDE)
formula_weight	925.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GGKKKYKL

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	399

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6. Citations (1)

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length_a	50.600 Å
length_b	81.400 Å
length_c	110.700 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	—

resolution	2.050 Å
resolution_low	14.000 Å
r_factor	0.1810
r_work	0.1810
r_free	—

fit	/app/data/saxs_computation/ag/1agd/1agd.fit
pddf	/app/data/pr_computation/ag/1agd/1agd.pr.out
profile	/app/data/saxs_computation/ag/1agd/1agd.dat

ANTAGONIST HIV-1 GAG PEPTIDES INDUCE STRUCTURAL CHANGES IN HLA B8-HIV-1 GAG PEPTIDE (GGKKKYKL-INDEX PEPTIDE)

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)