← Back to search

1ca8

Thrombin inhibitors with rigid tripeptidyl aldehydes

Method: X-RAY DIFFRACTION D_max: 68.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1ca8
deposition_date	1998-04-27
title	Thrombin inhibitors with rigid tripeptidyl aldehydes
keywords	SERINE PROTEASE, 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	18.56 Å
rg_electron	17.63 Å
i0	33710200.00
molecular_weight	30229.0 kDa
excluded_volume	29355 Å³
envelope_volume	44568 Å³
shell_volume	20401 Å³
envelope_diameter	58.8 Å
shell_rg	24.62 Å
envelope_rg	17.88 Å
shape_rg	17.60 Å
total_rg	18.38 Å
total_atoms	2276
n_residues	281
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	68.3 Å
rg_real	18.42 Å
rg_real_error	0.51 Å
i0_real	3.3710e+07
i0_real_error	4.1090e+05
rg_reciprocal	18.44 Å
i0_reciprocal	33710000.0000
total_estimate	0.7412
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	58.9 Å
skewness	0.096
kurtosis	-0.471
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	15040000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.552; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Thrombin light chain
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	2411

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

description	Thrombin heavy chain
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	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3S)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide
formula_weight	506.6 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	134

▶

6. Citations (1)

▶

length_a	71.130 Å
length_b	72.120 Å
length_c	73.140 Å
angle_alpha	90.00 °
angle_beta	100.80 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.100 Å
resolution_low	7.000 Å
r_factor	—
r_work	0.1570
r_free	—

fit	/app/data/saxs_computation/ca/1ca8/1ca8.fit
pddf	/app/data/pr_computation/ca/1ca8/1ca8.pr.out
profile	/app/data/saxs_computation/ca/1ca8/1ca8.dat

Thrombin inhibitors with 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)