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1e0f

Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor

Method: X-RAY DIFFRACTION D_max: 154.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e0f
deposition_date	2000-03-27
title	Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor
keywords	COAGULATION/CRYSTAL STRUCTURE/HEPARIN-B, COAGULATION/CRYSTAL STRUCTURE/HEPARIN-BINDING SITE/ HIRUDIN/THROMBIN INHIBITOR, HYDROLASE; HYDROLASE
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	43.51 Å
rg_electron	44.04 Å
i0	220203000.00
molecular_weight	119310.0 kDa
excluded_volume	148390 Å³
envelope_volume	207100 Å³
shell_volume	43618 Å³
envelope_diameter	150.5 Å
shell_rg	42.79 Å
envelope_rg	44.33 Å
shape_rg	44.04 Å
total_rg	43.96 Å
total_atoms	8374
n_residues	1048
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	154.6 Å
rg_real	44.14 Å
rg_real_error	1.88 Å
i0_real	2.2020e+08
i0_real_error	4.4630e+06
rg_reciprocal	43.51 Å
i0_reciprocal	220000000.0000
total_estimate	0.7214
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	30.1 Å
skewness	0.568
kurtosis	-0.580
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	57530000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.406; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.311; Smooth: 0.846

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	THROMBIN
formula_weight	4096.5 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	8441

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

description	THROMBIN
formula_weight	29792.3 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFIENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Entity 3 polymer

description	HAEMADIN
formula_weight	6262.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	I,J,K

IRFGMGKVPCPDGEVGYTCDCGEKICLYGQSCNDGQCSGDPKPSSEFEEFEIDEEEK

Source

organism	HAEMADIPSA SYLVESTRIS
ncbi_taxonomy_id	13555
host_organism	ESCHERICHIA COLI

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	67

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6. Citations (3)

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length_a	121.670 Å
length_b	50.570 Å
length_c	129.740 Å
angle_alpha	90.00 °
angle_beta	114.76 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 2 1
int_tables_number	3
crystal_system	—

resolution	3.100 Å
resolution_low	10.000 Å
r_factor	0.2080
r_work	0.2080
r_free	0.2550

fit	/app/data/saxs_computation/e0/1e0f/1e0f.fit
pddf	/app/data/pr_computation/e0/1e0f/1e0f.pr.out
profile	/app/data/saxs_computation/e0/1e0f/1e0f.dat

Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding 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 (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (3)

7. Files & Curves (10)

Files (7)

Curves (3)