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1d6w

STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTROPHILIC INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1

Method: X-RAY DIFFRACTION D_max: 58.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d6w
deposition_date	1999-10-15
title	STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTROPHILIC INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1
keywords	HYDROLASE, THROMBIN, THROMBIN 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	18.82 Å
rg_electron	17.86 Å
i0	37076800.00
molecular_weight	31546.0 kDa
excluded_volume	30518 Å³
envelope_volume	46481 Å³
shell_volume	20915 Å³
envelope_diameter	59.0 Å
shell_rg	24.97 Å
envelope_rg	18.19 Å
shape_rg	17.84 Å
total_rg	18.61 Å
total_atoms	2383
n_residues	287
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	58.8 Å
rg_real	18.67 Å
rg_real_error	0.20 Å
i0_real	3.7080e+07
i0_real_error	4.0070e+05
rg_reciprocal	18.70 Å
i0_reciprocal	37080000.0000
total_estimate	0.8930
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.2 Å
skewness	0.102
kurtosis	-0.461
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	13470000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	THROMBIN
formula_weight	33094.0 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2516

ADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

Entity 2 polymer

description	DECAPEPTIDE INHIBITOR
formula_weight	1363.4 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

DFEEIPEEYL

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	;(5S)-N-[trans-4-(2-amino-1H-imidazol-5-yl)cyclohexyl]-1,3-dioxo-2-[2-(phenylsulfonyl)ethyl]-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazine-5-carboxamide ;
formula_weight	527.6 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	133

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6. Citations (1)

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length_a	71.430 Å
length_b	71.670 Å
length_c	72.450 Å
angle_alpha	90.00 °
angle_beta	101.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.000 Å
resolution_low	9.000 Å
r_factor	0.1740
r_work	—
r_free	—

fit	/app/data/saxs_computation/d6/1d6w/1d6w.fit
pddf	/app/data/pr_computation/d6/1d6w/1d6w.pr.out
profile	/app/data/saxs_computation/d6/1d6w/1d6w.dat

STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTROPHILIC INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)