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9tjx

Structure of factor VII Gla domain bound to EPCR

Method: X-RAY DIFFRACTION D_max: 131.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tjx
deposition_date	2025-12-08
title	Structure of factor VII Gla domain bound to EPCR
keywords	Factor VII, activated factor VII, EPCR, GLA DOMAIN, COMPLEX, CALCIUM IONS, BLOOD CLOTTING; BLOOD CLOTTING
method	X-RAY DIFFRACTION

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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	39.67 Å
rg_electron	39.25 Å
i0	143531000.00
molecular_weight	96505.0 kDa
excluded_volume	120220 Å³
envelope_volume	169560 Å³
shell_volume	37202 Å³
envelope_diameter	127.1 Å
shell_rg	43.21 Å
envelope_rg	38.60 Å
shape_rg	39.19 Å
total_rg	39.72 Å
total_atoms	6756
n_residues	755
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	131.8 Å
rg_real	39.96 Å
rg_real_error	1.24 Å
i0_real	1.4350e+08
i0_real_error	2.4550e+06
rg_reciprocal	39.79 Å
i0_reciprocal	143500000.0000
total_estimate	0.7940
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.2 Å
skewness	0.354
kurtosis	-0.713
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	11760000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.815; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

Entity 1 polymer

description	Endothelial protein C receptor
formula_weight	22214.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	6759

GPSQDASDGLQRLHMLQISYFRDPYHVWYQGQASLGGHLTHVLEGPDTNTTIIQLQPLQEPESWARTQSGLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAVNGSSFVSFRPERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKHISAENTKGSQTSRSYTS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetus cricetus

Entity 2 polymer

description	Factor VII light chain
formula_weight	4190.3 kDa
src_method	syn
entity_count	4

Polymer

type	polypeptide(L)
strand_id	L,E,F,R

ANAFLEELRPGSLERECKEEQCSFEEAREIFK

Entity 3 branched

description	;alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	732.7 kDa
src_method	man
entity_count	1

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 5 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	1

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 7 non-polymer

description	PHOSPHATIDYLETHANOLAMINE
formula_weight	734.0 kDa
src_method	syn
entity_count	4

Entity 8 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	20

Entity 10 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	7

Entity 11 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 12 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	3

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6. Citations (1)

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length_a	278.406 Å
length_b	44.222 Å
length_c	111.252 Å
angle_alpha	90.00 °
angle_beta	93.01 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.000 Å
resolution_low	43.670 Å
r_factor	0.2442
r_work	0.2416
r_free	0.2954

fit	/app/data/saxs_computation/tj/9tjx/9tjx.fit
pddf	/app/data/pr_computation/tj/9tjx/9tjx.pr.out
profile	/app/data/saxs_computation/tj/9tjx/9tjx.dat

Structure of factor VII Gla domain bound to EPCR

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

Refinement

Diffraction

5. Entities & Polymer Info (12)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 branched

Entity 4 branched

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)