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1c5n

STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR

Method: X-RAY DIFFRACTION D_max: 59.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1c5n
deposition_date	1999-12-22
title	STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR
keywords	S1 site inhibitor, urokinase, trypsin, 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	19.37 Å
rg_electron	18.14 Å
i0	21300700.00
molecular_weight	34800.0 kDa
excluded_volume	43334 Å³
envelope_volume	48785 Å³
shell_volume	21577 Å³
envelope_diameter	61.3 Å
shell_rg	25.33 Å
envelope_rg	18.47 Å
shape_rg	18.13 Å
total_rg	19.12 Å
total_atoms	4812
n_residues	297
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	59.1 Å
rg_real	19.20 Å
rg_real_error	0.26 Å
i0_real	2.1300e+07
i0_real_error	2.4250e+05
rg_reciprocal	19.23 Å
i0_reciprocal	21300000.0000
total_estimate	0.8985
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.0 Å
skewness	0.085
kurtosis	-0.449
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	7833000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Thrombin light chain
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	5619

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

description	Thrombin heavy chain
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	Hirudin
formula_weight	1363.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

DFEEIPEEYL

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	4-IODOBENZO[B]THIOPHENE-2-CARBOXAMIDINE
formula_weight	303.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	255

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6. Citations (1)

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length_a	72.140 Å
length_b	72.260 Å
length_c	73.090 Å
angle_alpha	90.00 °
angle_beta	101.23 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.500 Å
resolution_low	7.500 Å
r_factor	0.2200
r_work	0.2200
r_free	0.2460

fit	/app/data/saxs_computation/c5/1c5n/1c5n.fit
pddf	/app/data/pr_computation/c5/1c5n/1c5n.pr.out
profile	/app/data/saxs_computation/c5/1c5n/1c5n.dat

STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR

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)