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1doj

Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A

Method: X-RAY DIFFRACTION D_max: 58.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1doj
deposition_date	1999-12-21
title	Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A
keywords	thrombin, serine protease, enzyme inhibition, 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	19.19 Å
rg_electron	18.00 Å
i0	21907900.00
molecular_weight	35706.0 kDa
excluded_volume	44622 Å³
envelope_volume	48704 Å³
shell_volume	21568 Å³
envelope_diameter	58.2 Å
shell_rg	25.29 Å
envelope_rg	18.42 Å
shape_rg	17.99 Å
total_rg	18.99 Å
total_atoms	2510
n_residues	303
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	58.1 Å
rg_real	19.02 Å
rg_real_error	0.29 Å
i0_real	2.1910e+07
i0_real_error	2.4630e+05
rg_reciprocal	19.05 Å
i0_reciprocal	21910000.0000
total_estimate	0.8213
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.0 Å
skewness	0.078
kurtosis	-0.465
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	8317000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	ALPHA-THROMBIN
formula_weight	33858.7 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2882

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Entity 2 polymer

description	HIRUGEN
formula_weight	1491.5 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

DFEEIPEEYLQ

Entity 3 non-polymer

description	N-methyl-D-phenylalanyl-N-{(1S)-4-carbamimidamido-1-[(6-carboxy-1,3-benzothiazol-2-yl)carbonyl]butyl}-L-prolinamide
formula_weight	593.7 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

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

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	349

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6. Citations (4)

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length_a	62.982 Å
length_b	117.521 Å
length_c	47.989 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.700 Å
resolution_low	8.000 Å
r_factor	0.1740
r_work	0.1740
r_free	0.2170

fit	/app/data/saxs_computation/do/1doj/1doj.fit
pddf	/app/data/pr_computation/do/1doj/1doj.pr.out
profile	/app/data/saxs_computation/do/1doj/1doj.dat

Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A

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 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (4)

7. Files & Curves (10)

Files (7)

Curves (3)