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1b5g

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

Method: X-RAY DIFFRACTION D_max: 58.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1b5g
deposition_date	1998-03-05
title	HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN
keywords	SERINE PROTEASE-INHIBITOR, 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	18.92 Å
rg_electron	17.92 Å
i0	37300900.00
molecular_weight	31672.0 kDa
excluded_volume	30662 Å³
envelope_volume	47089 Å³
shell_volume	21107 Å³
envelope_diameter	58.4 Å
shell_rg	25.02 Å
envelope_rg	18.23 Å
shape_rg	17.91 Å
total_rg	18.67 Å
total_atoms	2393
n_residues	288
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	58.6 Å
rg_real	18.76 Å
rg_real_error	0.20 Å
i0_real	3.7300e+07
i0_real_error	4.0840e+05
rg_reciprocal	18.79 Å
i0_reciprocal	37300000.0000
total_estimate	0.8946
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.4 Å
skewness	0.098
kurtosis	-0.475
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	13360000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.981

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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	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L
atom_count	2526

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	H

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Entity 3 polymer

description	HIRUGEN
formula_weight	1534.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

NGDFEEIPEEYL

Entity 4 non-polymer

description	;[[[(4S,5S)-4-[[(3S,6S,8aR)-6-azanyl-5-oxo-6-(phenylmethyl)-1,2,3,7,8,8a-hexahydroindolizin-3-yl]carbonylamino]-5-(1,3-b enzothiazol-2-yl)-5-hydroxy-pentyl]amino]-azanyl-methylidene]azanium ;
formula_weight	564.7 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	133

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6. Citations (3)

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length_a	70.840 Å
length_b	72.080 Å
length_c	73.000 Å
angle_alpha	90.00 °
angle_beta	100.90 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.070 Å
resolution_low	7.000 Å
r_factor	—
r_work	0.1640
r_free	—

fit	/app/data/saxs_computation/b5/1b5g/1b5g.fit
pddf	/app/data/pr_computation/b5/1b5g/1b5g.pr.out
profile	/app/data/saxs_computation/b5/1b5g/1b5g.dat

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

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

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (3)

7. Files & Curves (10)

Files (7)

Curves (3)