SAXSdb — 9yq8

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1. Structure Basics

entry_id	9yq8
deposition_date	2025-10-15
title	Cryo-EM complex of meizothrombinDESF1, factor Xa, and factor Va
keywords	Coagulation cascade, Serine Proteases, Thrombotic, Clotting Factors, BLOOD CLOTTING; BLOOD CLOTTING
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	42.62 Å
rg_electron	42.38 Å
i0	719439000.00
molecular_weight	219490.0 kDa
excluded_volume	273790 Å³
envelope_volume	368700 Å³
shell_volume	70531 Å³
envelope_diameter	141.7 Å
shell_rg	48.89 Å
envelope_rg	42.32 Å
shape_rg	42.39 Å
total_rg	42.67 Å
total_atoms	15452
n_residues	1921
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	136.2 Å
rg_real	42.53 Å
rg_real_error	1.06 Å
i0_real	7.1940e+08
i0_real_error	1.2610e+07
rg_reciprocal	42.62 Å
i0_reciprocal	719500000.0000
total_estimate	0.8944
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.5 Å
skewness	0.214
kurtosis	-0.576
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	114000000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.796

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Coagulation factor X
formula_weight	38589.3 kDa
ec_number	3.4.21.6
mutation	S379A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E
atom_count	15452

FTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLERRKRSVAQATSSSGEAPDSITWKPYDAADLDPTENPFDLLDFNQTQPERGDNNLTRIVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDAGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Mesocricetus auratus

Entity 2 polymer

description	Coagulation factor Va light chain
formula_weight	75283.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

SNNGNRRNYYIAAEEISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKRDPRGEYEEHLGILGPIIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEWFKEDNAVQPNSSYTYVWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICQKGILHKDSNMPMDMREFVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGMIYSLPGLKMYEQEWVRLHLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKTLEMKASKPGWWLLNTEVGENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGYWEPRLARLNNGGSYNAWSVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTTEFYVAYSSNQINWQIFKGNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNRPTLRLELQGCEVNGCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSMVDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY

Entity 3 polymer

description	Meizothrombin
formula_weight	16503.9 kDa
ec_number	3.4.21.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

VPDRGQQYQGRLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCYVAGKPGDFGYCDLNYCEEAVEEETGDGLDEDSDRAIEGRTATSEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYID

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Mesocricetus auratus

Entity 4 polymer

description	Thrombin heavy chain
formula_weight	29578.1 kDa
ec_number	3.4.21.5
mutation	S525A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Mesocricetus auratus

Entity 5 polymer

description	Coagulation factor V heavy chain
formula_weight	77205.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

AQLRQFYVAAQGISWSYRPEPTNSSLNLSVTSFKKIVYREYEPYFKKEKPQSTISGLLGPTLYAEVGDIIKVHFKNKADKPLSIHPQGIRYSKLSEGASYLDHTFPAEKMDDAVAPGREYTYEWSISEDSGPTHDDPPCLTHIYYSHENLIEDFNSGLIGPLLICKKGTLTEGGTQKTFDKQIVLLFAVFDESKSWSQSSSLMYTVNGYVNGTMPDITVCAHDHISWHLLGMSSGPELFSIHFNGQVLEQNHHKVSAITLVSATSTTANMTVGPEGKWIISSLTPKHLQAGMQAYIDIKNCPKKTRNLKKITREQRRHMKRWEYFIAAEEVIWDYAPVIPANMDKKYRSQHLDNFSNQIGKHYKKVMYTQYEDESFTKHTVNPNMKEDGILGPIIRAQVRDTLKIVFKNMASRPYSIYPHGVTFSPYEDEVNSSFTSGRNNTMIRAVQPGETYTYKWNILEFDEPTENDAQCLTRPYYSDVDIMRDIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDENKSWYLEDNINKFCENPDEVKRDDPKFYESNIMSTINGYVPESITTLGFCFDDTVQWHFCSVGTQNEILTIHFTGHSFIYGKRHEDTLTLFPMRGESVTVTMDNVGTWMLTSMNSSPRSKKLRLKFRDVKCIPDDDEDSYEIFEPPEST

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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	3.84 Å
resolution_method	—
num_particles	38200

fit	/app/data/saxs_computation/yq/9yq8/9yq8.fit
pddf	/app/data/pr_computation/yq/9yq8/9yq8.pr.out
profile	/app/data/saxs_computation/yq/9yq8/9yq8.dat

Cryo-EM complex of meizothrombinDESF1, factor Xa, and factor Va

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)