← Back to search

1eb1

Complex structure of human thrombin with N-methyl-arginine inhibitor

Method: X-RAY DIFFRACTION D_max: 57.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1eb1
deposition_date	2001-07-18
title	Complex structure of human thrombin with N-methyl-arginine inhibitor
keywords	SERINE PROTEINASE, BLOOD COAGULATION, CALCIUM-BINDING, GLYCOPROTEIN, KRINGLE, 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	19.16 Å
rg_electron	18.00 Å
i0	20137700.00
molecular_weight	34369.0 kDa
excluded_volume	43127 Å³
envelope_volume	48154 Å³
shell_volume	21397 Å³
envelope_diameter	59.0 Å
shell_rg	25.19 Å
envelope_rg	18.36 Å
shape_rg	17.99 Å
total_rg	19.00 Å
total_atoms	2419
n_residues	295
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	57.9 Å
rg_real	18.99 Å
rg_real_error	0.23 Å
i0_real	2.0140e+07
i0_real_error	2.0480e+05
rg_reciprocal	19.02 Å
i0_reciprocal	20140000.0000
total_estimate	0.8994
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.9 Å
skewness	0.073
kurtosis	-0.471
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	7855000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.981

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	PEPTIDE INHIBITOR
formula_weight	1209.3 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2739

DYEPIPEEAF

Entity 2 polymer

description	THROMBIN HEAVY CHAIN
formula_weight	29594.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

Entity 3 polymer

description	THROMBIN LIGHT CHAIN
formula_weight	3188.6 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

ADCGLRPLFEKKSLEDKTERELLESYI

Entity 4 polymer

description	3-CYCLOHEXYL-D-ALANYL-L-PROLYL-N~2~-METHYL-L-ARGININE
formula_weight	438.6 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

APR

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	320

▶

6. Citations (1)

▶

length_a	69.839 Å
length_b	71.508 Å
length_c	71.710 Å
angle_alpha	90.00 °
angle_beta	99.34 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.800 Å
resolution_low	16.740 Å
r_factor	0.1910
r_work	0.1910
r_free	0.2200

fit	/app/data/saxs_computation/eb/1eb1/1eb1.fit
pddf	/app/data/pr_computation/eb/1eb1/1eb1.pr.out
profile	/app/data/saxs_computation/eb/1eb1/1eb1.dat

Complex structure of human thrombin with N-methyl-arginine inhibitor

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 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)