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10qr

Structure of human VCP/p97 hexamer bound to ADP (DMSO control)

Method: ELECTRON MICROSCOPY D_max: 168.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10qr
deposition_date	2026-02-02
title	Structure of human VCP/p97 hexamer bound to ADP (DMSO control)
keywords	hexamer, VCP, p97, ADP, 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	53.54 Å
rg_electron	53.26 Å
i0	3576420000.00
molecular_weight	495260.0 kDa
excluded_volume	617960 Å³
envelope_volume	911180 Å³
shell_volume	134410 Å³
envelope_diameter	169.0 Å
shell_rg	61.58 Å
envelope_rg	52.76 Å
shape_rg	53.27 Å
total_rg	53.45 Å
total_atoms	34728
n_residues	4392
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	168.8 Å
rg_real	53.31 Å
rg_real_error	1.05 Å
i0_real	3.5760e+09
i0_real_error	7.7950e+07
rg_reciprocal	53.73 Å
i0_reciprocal	3579000000.0000
total_estimate	0.8749
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.0 Å
skewness	0.164
kurtosis	-0.478
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	463100000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.718

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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	34758

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	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	12

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	30

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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	2.30 Å
resolution_method	—
num_particles	201432

fit	/app/data/saxs_computation/0q/10qr/10qr.fit
pddf	/app/data/pr_computation/0q/10qr/10qr.pr.out
profile	/app/data/saxs_computation/0q/10qr/10qr.dat