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1awf

NOVEL COVALENT THROMBIN INHIBITOR FROM PLANT EXTRACT

Method: X-RAY DIFFRACTION D_max: 58.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1awf
deposition_date	1997-10-02
title	NOVEL COVALENT THROMBIN INHIBITOR FROM PLANT EXTRACT
keywords	PROTEINASE, BLOOD COAGULATION, TRYPSIN LIKE PROTEINASE, COMPLEX (PROTEASE-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	19.31 Å
rg_electron	18.07 Å
i0	20563200.00
molecular_weight	34860.0 kDa
excluded_volume	43765 Å³
envelope_volume	48662 Å³
shell_volume	21548 Å³
envelope_diameter	60.6 Å
shell_rg	25.28 Å
envelope_rg	18.41 Å
shape_rg	18.06 Å
total_rg	19.08 Å
total_atoms	2452
n_residues	294
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	58.4 Å
rg_real	19.14 Å
rg_real_error	0.22 Å
i0_real	2.0560e+07
i0_real_error	2.0190e+05
rg_reciprocal	19.17 Å
i0_reciprocal	20560000.0000
total_estimate	0.9000
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.7 Å
skewness	0.072
kurtosis	-0.477
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	8563000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	ALPHA THROMBIN
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	2682

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

description	ALPHA THROMBIN
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	HIRUGEN
formula_weight	1363.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

DFEEIPEEYL

Source

organism	Hirudo medicinalis
common_name	medicinal leech
ncbi_taxonomy_id	6421

Entity 4 non-polymer

description	;R3-ACETOXY-17-(1-FORMYL-5-METHYL-3-OXO-HEX-4-ENYL)-12,16-DIHYDROXY-14-HYDROXYMETHYL-4,10,13-TRIMETHYL-2,3,4,5,6,9,10,11,12,13,14,15,16,17-TETRADECAHYDRO-1H-CYCLOPENTA[A]PHENANTHRENE-4-CARBOXYLIC ACID IDOPYRANOSYL ESTER ;
formula_weight	736.8 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	230

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6. Citations (1)

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length_a	71.920 Å
length_b	71.840 Å
length_c	73.010 Å
angle_alpha	90.00 °
angle_beta	100.39 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.200 Å
resolution_low	15.000 Å
r_factor	0.1960
r_work	0.1960
r_free	—

fit	/app/data/saxs_computation/aw/1awf/1awf.fit
pddf	/app/data/pr_computation/aw/1awf/1awf.pr.out
profile	/app/data/saxs_computation/aw/1awf/1awf.dat

NOVEL COVALENT THROMBIN INHIBITOR FROM PLANT EXTRACT

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

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)