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1d3p

CRYSTAL STRUCTURE OF HUMAN APLHA-THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 3

Method: X-RAY DIFFRACTION D_max: 58.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d3p
deposition_date	1999-09-30
title	CRYSTAL STRUCTURE OF HUMAN APLHA-THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 3
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	19.41 Å
rg_electron	18.14 Å
i0	20178400.00
molecular_weight	34415.0 kDa
excluded_volume	43176 Å³
envelope_volume	48968 Å³
shell_volume	21630 Å³
envelope_diameter	58.9 Å
shell_rg	25.34 Å
envelope_rg	18.48 Å
shape_rg	18.13 Å
total_rg	19.18 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	58.7 Å
rg_real	19.24 Å
rg_real_error	0.21 Å
i0_real	2.0180e+07
i0_real_error	2.1770e+05
rg_reciprocal	19.27 Å
i0_reciprocal	20180000.0000
total_estimate	0.9018
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.6 Å
skewness	0.086
kurtosis	-0.470
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	8758000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

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	2532

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	3-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-BENZYL]-2-4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL] -BENZO[B]THIOPHEN-6-OL
formula_weight	543.7 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	113

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6. Citations (1)

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length_a	71.370 Å
length_b	72.010 Å
length_c	73.440 Å
angle_alpha	90.00 °
angle_beta	100.36 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.100 Å
resolution_low	20.000 Å
r_factor	0.1790
r_work	0.1790
r_free	0.2140

fit	/app/data/saxs_computation/d3/1d3p/1d3p.fit
pddf	/app/data/pr_computation/d3/1d3p/1d3p.pr.out
profile	/app/data/saxs_computation/d3/1d3p/1d3p.dat

CRYSTAL STRUCTURE OF HUMAN APLHA-THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 3

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 (7)

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

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)