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1d3d

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZOTHIOPHENE INHIBITOR 4

Method: X-RAY DIFFRACTION D_max: 58.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d3d
deposition_date	1999-09-29
title	CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZOTHIOPHENE INHIBITOR 4
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	19.32 Å
rg_electron	18.07 Å
i0	20263900.00
molecular_weight	34463.0 kDa
excluded_volume	43181 Å³
envelope_volume	48718 Å³
shell_volume	21559 Å³
envelope_diameter	58.9 Å
shell_rg	25.28 Å
envelope_rg	18.45 Å
shape_rg	18.06 Å
total_rg	19.09 Å
total_atoms	2418
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	58.4 Å
rg_real	19.15 Å
rg_real_error	0.19 Å
i0_real	2.0260e+07
i0_real_error	2.0410e+05
rg_reciprocal	19.18 Å
i0_reciprocal	20260000.0000
total_estimate	0.8997
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.5 Å
skewness	0.088
kurtosis	-0.467
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	8837000.0000
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: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	ALPHA-THROMBIN
formula_weight	3317.7 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2537

EADCGLRPLFEKKSLEDKTERELLESYI

Entity 2 polymer

description	ALPHA-THROMBIN
formula_weight	29594.1 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

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-(3-BROMO-4-PYRROLIDIN-1-YLMETHYL-BENZYL)-2-[4-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-BENZO[B]THIOPHEN-6-OL
formula_weight	591.6 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	119

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6. Citations (1)

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length_a	71.110 Å
length_b	71.888 Å
length_c	73.321 Å
angle_alpha	90.00 °
angle_beta	100.60 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.040 Å
resolution_low	20.000 Å
r_factor	0.1750
r_work	0.1750
r_free	0.2230

fit	/app/data/saxs_computation/d3/1d3d/1d3d.fit
pddf	/app/data/pr_computation/d3/1d3d/1d3d.pr.out
profile	/app/data/saxs_computation/d3/1d3d/1d3d.dat

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZOTHIOPHENE INHIBITOR 4

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

Entity 2 polymer

Polymer

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)