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9yp8

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

Method: ELECTRON MICROSCOPY D_max: 272.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yp8
deposition_date	2025-10-13
title	Structure of human VCP/p97 dodecamer bound to ADP and UTE-156
keywords	inhibitor, UTE-156, VCP, p97, covalent, dodecamer, 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	70.82 Å
rg_electron	70.54 Å
i0	27881700000.00
molecular_weight	921950.0 kDa
excluded_volume	883740 Å³
envelope_volume	1985200 Å³
shell_volume	223250 Å³
envelope_diameter	225.8 Å
shell_rg	77.92 Å
envelope_rg	69.14 Å
shape_rg	70.48 Å
total_rg	70.70 Å
total_atoms	69864
n_residues	8808
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	272.4 Å
rg_real	75.09 Å
rg_real_error	1.89 Å
i0_real	2.8120e+10
i0_real_error	5.8290e+08
rg_reciprocal	71.40 Å
i0_reciprocal	27920000000.0000
total_estimate	0.8704
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	86.7 Å
skewness	0.630
kurtosis	0.572
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.8431
highest_alpha	1804000000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.640; Stabil: 0.855; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.900

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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	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	69888

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	12

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	syn
entity_count	12

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	24

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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	2.40 Å
resolution_method	—
num_particles	117690

fit	/app/data/saxs_computation/yp/9yp8/9yp8.fit
pddf	/app/data/pr_computation/yp/9yp8/9yp8.pr.out
profile	/app/data/saxs_computation/yp/9yp8/9yp8.dat