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9yp6

Structure of human VCP/p97 hexamer bound to ADP and UTE-156

Method: ELECTRON MICROSCOPY D_max: 171.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yp6
deposition_date	2025-10-13
title	Structure of human VCP/p97 hexamer bound to ADP and UTE-156
keywords	inhibitor, UTE-156, VCP, p97, covalent, hexamer, CHAPERONE; CHAPERONE
method	ELECTRON MICROSCOPY

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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	54.06 Å
rg_electron	53.75 Å
i0	7087140000.00
molecular_weight	460970.0 kDa
excluded_volume	441870 Å³
envelope_volume	925460 Å³
shell_volume	136170 Å³
envelope_diameter	172.6 Å
shell_rg	61.87 Å
envelope_rg	52.82 Å
shape_rg	53.73 Å
total_rg	53.92 Å
total_atoms	34932
n_residues	4404
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	171.8 Å
rg_real	53.82 Å
rg_real_error	0.96 Å
i0_real	7.0870e+09
i0_real_error	1.2870e+08
rg_reciprocal	54.26 Å
i0_reciprocal	7092000000.0000
total_estimate	0.8786
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	65.2 Å
skewness	0.159
kurtosis	-0.478
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0001
highest_alpha	418400000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.798

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Transitional endoplasmic reticulum ATPase
formula_weight	89436.8 kDa
ec_number	3.6.4.6
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	34944

MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	N-(3-{[(6P)-2-(methanesulfonyl)-6-(1-methyl-1H-pyrazol-4-yl)pyrimidin-4-yl]amino}phenyl)prop-2-enamide
formula_weight	398.4 kDa
src_method	nat
entity_count	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	12

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.80 Å
resolution_method	—
num_particles	204722

fit	/app/data/saxs_computation/yp/9yp6/9yp6.fit
pddf	/app/data/pr_computation/yp/9yp6/9yp6.pr.out
profile	/app/data/saxs_computation/yp/9yp6/9yp6.dat