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1d3t

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 1

Method: X-RAY DIFFRACTION D_max: 57.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d3t
deposition_date	1999-09-30
title	CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 1
keywords	THROMBIN; BENZO[B]THIOPHENE, BLOOD CLOTTING, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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	19.34 Å
rg_electron	18.10 Å
i0	20122900.00
molecular_weight	34413.0 kDa
excluded_volume	43166 Å³
envelope_volume	48644 Å³
shell_volume	21537 Å³
envelope_diameter	58.6 Å
shell_rg	25.27 Å
envelope_rg	18.44 Å
shape_rg	18.08 Å
total_rg	19.13 Å
total_atoms	2419
n_residues	289
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	57.9 Å
rg_real	19.17 Å
rg_real_error	0.22 Å
i0_real	2.0120e+07
i0_real_error	2.3090e+05
rg_reciprocal	19.20 Å
i0_reciprocal	20120000.0000
total_estimate	0.9023
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.3 Å
skewness	0.085
kurtosis	-0.472
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	8550000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.974

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	ALPHA-THROMBIN
formula_weight	4096.5 kDa
ec_number	3.4.21.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2419

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 2 polymer

description	ALPHA-THROMBIN
formula_weight	29780.2 kDa
ec_number	3.4.21.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 3 polymer

description	HIRUGEN
formula_weight	1548.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

GDFEEIPEEYLQ

Entity 4 non-polymer

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

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	{2-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-BENZO[B]THIOPHEN-3-YL}-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-METHANONE
formula_weight	541.7 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	71.140 Å
length_b	71.850 Å
length_c	72.960 Å
angle_alpha	90.00 °
angle_beta	100.50 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	3.000 Å
resolution_low	20.000 Å
r_factor	0.1720
r_work	0.1720
r_free	0.2350

fit	/app/data/saxs_computation/d3/1d3t/1d3t.fit
pddf	/app/data/pr_computation/d3/1d3t/1d3t.pr.out
profile	/app/data/saxs_computation/d3/1d3t/1d3t.dat

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 1

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)