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1c5o

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

Method: X-RAY DIFFRACTION D_max: 59.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1c5o
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	selective, S1 site inhibitor, structure-based drug design, urokinase, trypsin, thrombin, BLOOD CLOTTING-HYDROLASE INHIBITOR COMPLEX; BLOOD CLOTTING/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	19.34 Å
rg_electron	18.09 Å
i0	20915500.00
molecular_weight	34705.0 kDa
excluded_volume	43343 Å³
envelope_volume	48301 Å³
shell_volume	21427 Å³
envelope_diameter	61.0 Å
shell_rg	25.25 Å
envelope_rg	18.44 Å
shape_rg	18.08 Å
total_rg	19.07 Å
total_atoms	4825
n_residues	298
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	59.0 Å
rg_real	19.17 Å
rg_real_error	0.22 Å
i0_real	2.0920e+07
i0_real_error	2.4660e+05
rg_reciprocal	19.20 Å
i0_reciprocal	20920000.0000
total_estimate	0.7501
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.9 Å
skewness	0.095
kurtosis	-0.444
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	7887000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 0.356; Positv: 1.000; Valcen: 0.982; Smooth: 0.993

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	6121

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	1491.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

DFEEIPEEYLQ

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	BENZAMIDINE
formula_weight	120.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	426

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6. Citations (1)

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length_a	71.460 Å
length_b	71.820 Å
length_c	72.850 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	1.900 Å
resolution_low	7.500 Å
r_factor	0.2000
r_work	0.2000
r_free	0.2620

fit	/app/data/saxs_computation/c5/1c5o/1c5o.fit
pddf	/app/data/pr_computation/c5/1c5o/1c5o.pr.out
profile	/app/data/saxs_computation/c5/1c5o/1c5o.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 (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 (1)

7. Files & Curves (10)

Files (7)

Curves (3)