SAXSdb — 9ut4

▼

1. Structure Basics

entry_id	9ut4
deposition_date	2025-05-02
title	The primase module of the helicase-primase complex from HHV1 bound with ssDNA and amenamevir
keywords	Helicase, Primase, Inhibitor Complex, Herpesvirus, REPLICATION; REPLICATION
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	40.32 Å
rg_electron	40.06 Å
i0	214977000.00
molecular_weight	121860.0 kDa
excluded_volume	153690 Å³
envelope_volume	204290 Å³
shell_volume	44346 Å³
envelope_diameter	136.9 Å
shell_rg	43.37 Å
envelope_rg	39.49 Å
shape_rg	40.03 Å
total_rg	40.39 Å
total_atoms	8607
n_residues	1138
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

▼

3. P(r) Analysis (GNOM)

dmax	133.5 Å
rg_real	40.49 Å
rg_real_error	1.16 Å
i0_real	2.1500e+08
i0_real_error	3.4550e+06
rg_reciprocal	40.33 Å
i0_reciprocal	214900000.0000
total_estimate	0.8503
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	37.7 Å
skewness	0.399
kurtosis	-0.554
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	34620000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.827; Smooth: 0.596

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Ubiquitin-like protein SMT3,DNA primase
formula_weight	130399.0 kDa
ec_number	2.7.7.-
mutation	R64T/R71E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	8607

MSYYHHHHHHDYDIPTTENLYFQGITSLYKKAGFLQLGSLQDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGGMGQEDGNRGERRAAGTPVEVTALYATDGCVITSSIALLTNSLLGAEPVYIFSYDAYTHDGRADGPTEQDRFEESRALYQASGGLNGDSFRVTFCLLGTEVGGTHQARGRTRPMFVCRFERADDVAALQDALAHGTPLQPDHIAATLDAEATFALHANMILALTVAINNASPRTGRDAAAAQYDQGASLRSLVGRTSLGQRGLTTLYVHHEVRVLAAYRRAYYGSAQSPFWFLSKFGPDEKSLVLTTRYYLLQAQRLGGAGATYDLQAIKDICATYAIPHAPRPDTVSAASLTSFAAITRFCCTSQYARGAAAAGFPLYVERRIAADVRETSALEKFITHDRSCLRVSDREFITYIYLAHFECFSPPRLATHLRAVTTHDPNPAASTEQPSPLGREAVEQFFCHVRAQLNIGEYVKHNVTPRETVLDGDTAKAYLRARTYAPGALTPAPAYCGAVDSATKMMGRLADAEKLLVPRGWPAFAPASPGEDTAGGTPPPQTCGIVKRLLRLAATEQQGPTPPAIAALIRNAAVQTPLPVYRISMVPTGQAFAALAWDDWARITRDARLAEAVVSAEAAAHPDHGALGRRLTDRIRAQGPVMPPGGLDAGGQMYVNRNEIFNGALAITNIILDLDIALKEPVPFRRLHEALGHFRRGALAAVQLLFPAARVDPDAYPCYFFKSACRPGPASVGSGSGLGNDDDGDWFPCYDDAGDEEWAEDPGAMDTSHDPPDDEVAYFDLCHEVGPTAEPRETDSPVCSCTDKIGLRVCMPVPAPYVVHGSLTMRGVARVIQQAVLLDRDFVEAIGSYVKNFLLIDTGVYAHGHSLRLPYFAKIAPDGPACGRLLPVFVIPPACKDVPAFVAAHADPRRFHFHAPPTYLASPREIRVLHSLGGDYVSFFERKASRNALEHFGRRETLTEVLGRYNVQPDAGGTVEGFASELLGRIVACIETHFPEHAGEYQAVSVRRAVSKDDWVLLQLVPVRGTLQQSLSCLRFKHGRASRATARTFVALSVGANNRLCVSLCQQCFAAKCDSNRLHTLFTIDAGTPCSPSVPCSTSQPSS

Source

organism	Human alphaherpesvirus 1
common_name	Herpes simplex virus type 1
ncbi_taxonomy_id	10298
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein
formula_weight	95846.4 kDa
mutation	R64T/R71E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MSYYHHHHHHDYDIPTTENLYFQGITSLYKKAGFLQLGSLQDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGGMDTADIVWVEESVSAITLYAVWLPPRAREYFHALVYFVCRNAAGEGRARFAEVSVTATELRDFYGSADVSVQAVVAAARAATTPAASPLEPLENPTLWRALYACVLAALERQTGPVALFAPLRIGSDPRTGLVVKVERASWGPPAAPRAALLVAEANIDIDPMALAARVAEHPDARLAWARLAAIRDTPQCASAASLTVNITTGTALFAREYQTLAFPPIKKEGAFGDLVEVCEVGLRPRGHPQRVTARVLLPRDYDYFVSAGEKFSAPALVALFRQWHTTVHAAPGALAPVFAFLGPEFEVRGGPVPYFAVLGFPGWPTFTVPATAESARDLVRGAAAAYAALLGAWPAVGARVVLPPRAWPGVASAAAGCLLPAVREAVARWHPATKIIQLLDPPAAVGPVWTARFCFPGLRAQLLAALADLGGSGLADPHGRTGLARLDALVVAAPSEPWAGAVLERLVPDTCNACPALRQLLGGVMAAVCLQIEETASSVKFAVCGGDGGAFWGVFNVDPQDADAASGVIEDARRAIETAVGAVLRANAVRLRHPLCLALEGVYTHAVAWSQAGVWFWNSRDNTDHLGGFPLRGPAYTTAAGVVRDTLRRVLGLTTACVPEEDALTARGLMEDACDRLILDAFNKRLDAEYWSVRVSPFEASDPLPPTAFRGGALLDAEHYWRRVVRVCPGGGESVGVPVDLYPRPLVLPPVDCAHHLREILREIELVFTGVLAGVWGEGGKFVYPFDDKMSFLFA

Source

organism	Human alphaherpesvirus 1
common_name	Herpes simplex virus type 1
ncbi_taxonomy_id	10298
host_organism	Spodoptera frugiperda

▶

6. Citations (1)

▶

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	triclinic

resolution	2.91 Å
resolution_method	—
num_particles	467989

fit	/app/data/saxs_computation/ut/9ut4/9ut4.fit
pddf	/app/data/pr_computation/ut/9ut4/9ut4.pr.out
profile	/app/data/saxs_computation/ut/9ut4/9ut4.dat

The primase module of the helicase-primase complex from HHV1 bound with ssDNA and amenamevir

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)