← Back to search

1d3q

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 2

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

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1d3q
deposition_date	1999-09-30
title	CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 2
keywords	THROMBIN; BENZO[B]THIOPHENE, BLOOD CLOTTING, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	19.35 Å
rg_electron	18.09 Å
i0	20009300.00
molecular_weight	34398.0 kDa
excluded_volume	43186 Å³
envelope_volume	48689 Å³
shell_volume	21551 Å³
envelope_diameter	58.7 Å
shell_rg	25.28 Å
envelope_rg	18.44 Å
shape_rg	18.08 Å
total_rg	19.12 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

▼

3. P(r) Analysis (GNOM)

dmax	58.4 Å
rg_real	19.18 Å
rg_real_error	0.24 Å
i0_real	2.0010e+07
i0_real_error	2.4970e+05
rg_reciprocal	19.21 Å
i0_reciprocal	20010000.0000
total_estimate	0.9022
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.5 Å
skewness	0.086
kurtosis	-0.470
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	8566000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.995

▶

4. Crystallography & Experiment

▶

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	2418

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]THIOPHENE
formula_weight	526.7 kDa
src_method	syn
entity_count	1

▶

6. Citations (1)

▶

length_a	71.150 Å
length_b	71.730 Å
length_c	73.100 Å
angle_alpha	90.00 °
angle_beta	100.56 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.900 Å
resolution_low	20.000 Å
r_factor	0.1670
r_work	0.1670
r_free	0.2280

fit	/app/data/saxs_computation/d3/1d3q/1d3q.fit
pddf	/app/data/pr_computation/d3/1d3q/1d3q.pr.out
profile	/app/data/saxs_computation/d3/1d3q/1d3q.dat

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 2

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)