← Back to search

1ad8

COMPLEX OF THROMBIN WITH AND INHIBITOR CONTAINING A NOVEL P1 MOIETY

Method: X-RAY DIFFRACTION D_max: 58.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1ad8
deposition_date	1997-02-24
title	COMPLEX OF THROMBIN WITH AND INHIBITOR CONTAINING A NOVEL P1 MOIETY
keywords	COMPLEX (SERINE PROTEASE-INHIBITOR), HYDROLASE, SERINE PROTEASE, COAGULANT, INHIBITOR, 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	19.13 Å
rg_electron	17.92 Å
i0	19786500.00
molecular_weight	33923.0 kDa
excluded_volume	42466 Å³
envelope_volume	47319 Å³
shell_volume	21159 Å³
envelope_diameter	59.8 Å
shell_rg	25.05 Å
envelope_rg	18.28 Å
shape_rg	17.91 Å
total_rg	18.93 Å
total_atoms	2385
n_residues	287
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	58.6 Å
rg_real	18.97 Å
rg_real_error	0.20 Å
i0_real	1.9790e+07
i0_real_error	1.9560e+05
rg_reciprocal	18.99 Å
i0_reciprocal	19790000.0000
total_estimate	0.8978
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.2 Å
skewness	0.088
kurtosis	-0.462
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	7569000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.989

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	THROMBIN (SMALL SUBUNIT)
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	2587

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

description	THROMBIN (LARGE SUBUNIT)
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	HIRUDIN (53-65) PEPTIDE
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	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	[DEHYDROXY-N-METHYL-TYROSYL-PROLINYL]-[4,4,5,5,5-PENTAFLUORO-3-OXY-1-[3-INDOLYL]-PENT-2-YL]AMINE
formula_weight	564.5 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	195

▶

6. Citations (1)

▶

length_a	70.550 Å
length_b	72.050 Å
length_c	73.000 Å
angle_alpha	90.00 °
angle_beta	101.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.000 Å
resolution_low	8.000 Å
r_factor	0.2050
r_work	0.2050
r_free	—

fit	/app/data/saxs_computation/ad/1ad8/1ad8.fit
pddf	/app/data/pr_computation/ad/1ad8/1ad8.pr.out
profile	/app/data/saxs_computation/ad/1ad8/1ad8.dat

COMPLEX OF THROMBIN WITH AND INHIBITOR CONTAINING A NOVEL P1 MOIETY

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)