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9td3

ERAP1 in complex with 1-[2-(6-bromo-2,2-difluoro-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-4-yl)acetamido]cyclohexane-1-carboxylic acid

Method: X-RAY DIFFRACTION D_max: 91.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9td3
deposition_date	2025-11-22
title	ERAP1 in complex with 1-[2-(6-bromo-2,2-difluoro-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-4-yl)acetamido]cyclohexane-1-carboxylic acid
keywords	ERAP1, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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	28.76 Å
rg_electron	28.06 Å
i0	292507000.00
molecular_weight	92489.0 kDa
excluded_volume	90027 Å³
envelope_volume	148540 Å³
shell_volume	42617 Å³
envelope_diameter	96.0 Å
shell_rg	36.69 Å
envelope_rg	28.23 Å
shape_rg	28.09 Å
total_rg	28.57 Å
total_atoms	7004
n_residues	857
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	91.9 Å
rg_real	28.67 Å
rg_real_error	0.64 Å
i0_real	2.9250e+08
i0_real_error	4.8040e+06
rg_reciprocal	28.71 Å
i0_reciprocal	292500000.0000
total_estimate	0.8886
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.8 Å
skewness	0.288
kurtosis	-0.278
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	90180000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.943

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Endoplasmic reticulum aminopeptidase 1
formula_weight	105371.4 kDa
ec_number	3.4.11.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8325

MVFLPLKWSLATMSFLLSSLLALLTVSTPSWCQSTEASPKRSDGTPFPWNKIRLPEYVIPVHYDLLIHAQLTTLTFWGTTKVEITASQPTSTIILHSHHLQISRATLRKGAGERLSEEPLQVLEHPRQEQIALLAPEPLLVGLPYTVVIHYAGQLSETFHGFYKSTYRTKEGELRILASTQFEPTAARMAFPCFDEPAFKASFSIKIRREPRHLAISNMPLVKSVTVAEGLIEDHFDVTVKMSTYLVAFIISDFESVSKITKSGVKVSVYAVPDKINQADYALDAAVTLLEFYEDYFSIPYPLPKQDLAAIPDFQSGAMENWGLTTYRESALLFDAEKSSASSKLGITMTVAHELAHQWFGNLVTMEWWNDLWLNEGFAKFMEFVSVSVTHPELKVGDYFFGKCFDAMEVDALQSSHPVSTPVENPAQIREMFDDVSYDKGACILNMLREYLSADAFKSGIVQYLQKHSYKNTKNEDLWDSMASIGSGGVDVKTMMNTWTLQRGFPLITITVRGRNVHMKQEHYMKGSDGAPDTGYLWHVPLTFITSKSDMVHRFLLKTKTDVLILPEEVEWIKFNVGMNGYYIVHYEDDGWDSLTGLLKGTHTAVSSNDRASLINNAFQLVSIGKLSIEKALDLSLYLKHETEIMPVFQGLNELIPMYKLMEKRDMNEVETQFKAFLIRLLRDLIDKQTWTDEGSVSERMLRSQLLLLACVHNYQPCVQRAEGYFRKWKESNGQLSLPVDVTLAVFAVGAQSTEGWDFLYSKYQFSLSSTEKSQIEFALCRTQNKEKLQWLLDESFKGDKIKTQEFPQILTLIGRNPVGYPLAWQFLRKNWNKLVQKFELGSSSIAHMVMGTTNQFSTRTRLEEVKGFFSSLKENGSQLRCVQQTIETIEENIGWMDKNFDKIRVWLQSEKLERMENLYFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	11

Entity 5 non-polymer

description	1-[2-[6-bromanyl-2,2-bis(fluoranyl)-3-oxidanylidene-1,4-benzoxazin-4-yl]ethanoylamino]cyclohexane-1-carboxylic acid
formula_weight	447.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1245

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6. Citations (1)

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length_a	112.877 Å
length_b	140.457 Å
length_c	57.660 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.570 Å
resolution_low	52.370 Å
r_factor	0.1670
r_work	0.1660
r_free	0.1980

fit	/app/data/saxs_computation/td/9td3/9td3.fit
pddf	/app/data/pr_computation/td/9td3/9td3.pr.out
profile	/app/data/saxs_computation/td/9td3/9td3.dat