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1ba8

THROMBIN INHIBITOR WITH A RIGID TRIPEPTIDYL ALDEHYDES

Method: X-RAY DIFFRACTION D_max: 57.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ba8
deposition_date	1998-04-23
title	THROMBIN INHIBITOR WITH A RIGID TRIPEPTIDYL ALDEHYDES
keywords	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	18.89 Å
rg_electron	17.91 Å
i0	37673700.00
molecular_weight	31672.0 kDa
excluded_volume	30546 Å³
envelope_volume	47359 Å³
shell_volume	21211 Å³
envelope_diameter	58.8 Å
shell_rg	25.00 Å
envelope_rg	18.21 Å
shape_rg	17.90 Å
total_rg	18.63 Å
total_atoms	2393
n_residues	289
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	57.1 Å
rg_real	18.73 Å
rg_real_error	0.23 Å
i0_real	3.7670e+07
i0_real_error	4.2020e+05
rg_reciprocal	18.75 Å
i0_reciprocal	37670000.0000
total_estimate	0.9013
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.6 Å
skewness	0.086
kurtosis	-0.481
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	13490000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	THROMBIN
formula_weight	4096.5 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2551

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

description	THROMBIN
formula_weight	29780.2 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Entity 3 polymer

description	HIRUGEN
formula_weight	1561.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

XDGDFEEIPEEYL

Source

organism	Hirudo medicinalis
common_name	medicinal leech
ncbi_taxonomy_id	6421

Entity 4 non-polymer

description	amino({(4S)-4-[({(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}acetyl)amino]-5-oxopentyl}amino)methaniminium
formula_weight	467.6 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	158

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6. Citations (1)

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length_a	71.260 Å
length_b	72.290 Å
length_c	72.990 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	1.800 Å
resolution_low	7.000 Å
r_factor	—
r_work	0.1520
r_free	—

fit	/app/data/saxs_computation/ba/1ba8/1ba8.fit
pddf	/app/data/pr_computation/ba/1ba8/1ba8.pr.out
profile	/app/data/saxs_computation/ba/1ba8/1ba8.dat

THROMBIN INHIBITOR WITH A RIGID TRIPEPTIDYL ALDEHYDES

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

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)