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9td4

ERAP1 in complex with 1-[2-(2-oxo-5-phenyl-2,3-dihydro-1,3-benzoxazol-3-yl)acetamido]cyclohexane-1-carboxylic acid

Method: X-RAY DIFFRACTION D_max: 91.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9td4
deposition_date	2025-11-22
title	ERAP1 in complex with 1-[2-(2-oxo-5-phenyl-2,3-dihydro-1,3-benzoxazol-3-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	28.80 Å
rg_electron	28.08 Å
i0	294599000.00
molecular_weight	93066.0 kDa
excluded_volume	90710 Å³
envelope_volume	148610 Å³
shell_volume	42620 Å³
envelope_diameter	96.0 Å
shell_rg	36.75 Å
envelope_rg	28.24 Å
shape_rg	28.10 Å
total_rg	28.60 Å
total_atoms	7056
n_residues	862
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	91.2 Å
rg_real	28.71 Å
rg_real_error	0.56 Å
i0_real	2.9460e+08
i0_real_error	4.0920e+06
rg_reciprocal	28.75 Å
i0_reciprocal	294600000.0000
total_estimate	0.8916
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.290
kurtosis	-0.281
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	78390000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.938

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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	8387

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	D-MALATE
formula_weight	134.1 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	13

Entity 5 non-polymer

description	1-[2-(2-oxidanylidene-5-phenyl-1,3-benzoxazol-3-yl)ethanoylamino]cyclohexane-1-carboxylic acid
formula_weight	394.4 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1266

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6. Citations (1)

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length_a	112.759 Å
length_b	140.562 Å
length_c	57.613 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	1.730 Å
resolution_low	52.330 Å
r_factor	0.1630
r_work	0.1610
r_free	0.2000

fit	/app/data/saxs_computation/td/9td4/9td4.fit
pddf	/app/data/pr_computation/td/9td4/9td4.pr.out
profile	/app/data/saxs_computation/td/9td4/9td4.dat