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1bb0

THROMBIN INHIBITORS WITH RIGID TRIPEPTIDYL ALDEHYDES

Method: X-RAY DIFFRACTION D_max: 58.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1bb0
deposition_date	1998-04-28
title	THROMBIN INHIBITORS WITH 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	18.56 Å
rg_electron	17.61 Å
i0	33690000.00
molecular_weight	30127.0 kDa
excluded_volume	29209 Å³
envelope_volume	44541 Å³
shell_volume	20394 Å³
envelope_diameter	58.7 Å
shell_rg	24.60 Å
envelope_rg	17.87 Å
shape_rg	17.60 Å
total_rg	18.35 Å
total_atoms	2278
n_residues	282
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	58.2 Å
rg_real	18.41 Å
rg_real_error	0.23 Å
i0_real	3.3690e+07
i0_real_error	3.4840e+05
rg_reciprocal	18.43 Å
i0_reciprocal	33690000.0000
total_estimate	0.6737
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	23.9 Å
skewness	0.093
kurtosis	-0.470
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	13130000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 0.999; Sysdev: 0.391; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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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	2412

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	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-[(3R)-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

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6. Citations (1)

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length_a	71.140 Å
length_b	72.260 Å
length_c	72.730 Å
angle_alpha	90.00 °
angle_beta	100.70 °
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/bb/1bb0/1bb0.fit
pddf	/app/data/pr_computation/bb/1bb0/1bb0.pr.out
profile	/app/data/saxs_computation/bb/1bb0/1bb0.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)