SAXSdb — 9r8q

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1. Structure Basics

entry_id	9r8q
deposition_date	2025-05-16
title	Structure of thrombin bound to BAY 3389934
keywords	Blood coagulation, Protease, HYDROLASE; HYDROLASE
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	19.06 Å
rg_electron	18.06 Å
i0	39259500.00
molecular_weight	32354.0 kDa
excluded_volume	31195 Å³
envelope_volume	48789 Å³
shell_volume	21578 Å³
envelope_diameter	60.5 Å
shell_rg	25.32 Å
envelope_rg	18.44 Å
shape_rg	18.05 Å
total_rg	18.80 Å
total_atoms	2435
n_residues	287
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	58.5 Å
rg_real	18.90 Å
rg_real_error	0.26 Å
i0_real	3.9260e+07
i0_real_error	4.1070e+05
rg_reciprocal	18.93 Å
i0_reciprocal	39260000.0000
total_estimate	0.8943
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.4 Å
skewness	0.104
kurtosis	-0.473
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	14260000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.945

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Prothrombin
formula_weight	3432.8 kDa
ec_number	3.4.21.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L
atom_count	2666

EADCGLRPLFEKKSLEDKTERELLESYID

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Bos taurus

Entity 2 polymer

description	Prothrombin
formula_weight	29780.2 kDa
ec_number	3.4.21.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Bos taurus

Entity 3 polymer

description	Hirudin-2
formula_weight	1420.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

GDFEEIPEEYL

Source

organism	Hirudo medicinalis
common_name	medicinal leech
ncbi_taxonomy_id	6421
host_organism	synthetic construct

Entity 4 non-polymer

description	;2-(1-methylimidazol-2-yl)ethyl (2~{S})-3-[(5-chloranylthiophen-2-yl)carbonylamino]-2-[[2-ethyl-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-pyrrolidin-1-yl]phenyl]sulfonylamino]propanoate ;
formula_weight	624.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

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

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	4

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	223

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6. Citations (1)

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length_a	69.766 Å
length_b	71.817 Å
length_c	72.026 Å
angle_alpha	90.00 °
angle_beta	99.97 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.800 Å
resolution_low	23.650 Å
r_factor	0.1772
r_work	0.1759
r_free	0.2003

fit	/app/data/saxs_computation/r8/9r8q/9r8q.fit
pddf	/app/data/pr_computation/r8/9r8q/9r8q.pr.out
profile	/app/data/saxs_computation/r8/9r8q/9r8q.dat

Structure of thrombin bound to BAY 3389934

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)