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1d4p

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH 5-AMIDINOINDOLE-4-BENZYLPIPERIDINE INHIBITOR

Method: X-RAY DIFFRACTION D_max: 73.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d4p
deposition_date	1999-10-04
title	CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH 5-AMIDINOINDOLE-4-BENZYLPIPERIDINE INHIBITOR
keywords	THROMBIN; NONPEPTIDYL INHIBITOR; STRUCTURE-BASED DRUG DESIGN, BLOOD CLOTTING, 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	19.34 Å
rg_electron	18.10 Å
i0	19989500.00
molecular_weight	34215.0 kDa
excluded_volume	42897 Å³
envelope_volume	48678 Å³
shell_volume	21519 Å³
envelope_diameter	59.2 Å
shell_rg	25.27 Å
envelope_rg	18.49 Å
shape_rg	18.09 Å
total_rg	19.13 Å
total_atoms	2406
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	73.5 Å
rg_real	20.18 Å
rg_real_error	0.23 Å
i0_real	2.0050e+07
i0_real_error	1.9690e+05
rg_reciprocal	19.20 Å
i0_reciprocal	19990000.0000
total_estimate	0.6039
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	24.8 Å
skewness	0.597
kurtosis	0.857
angular_range	— – 0.4100 Å⁻¹
current_alpha	4.2270
highest_alpha	10280000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.542; Stabil: 0.893; Sysdev: 0.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.639

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	ALPHA-THROMBIN
formula_weight	4096.5 kDa
ec_number	3.4.21.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2522

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 2 polymer

description	ALPHA-THROMBIN
formula_weight	29780.2 kDa
ec_number	3.4.21.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 3 polymer

description	HIRUGEN
formula_weight	1548.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

GDFEEIPEEYLQ

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 non-polymer

description	2-(4-benzylpiperidine-1-carbonyl)-1H-indole-5-carboximidamide
formula_weight	360.5 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	116

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6. Citations (1)

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length_a	71.560 Å
length_b	72.060 Å
length_c	73.220 Å
angle_alpha	90.00 °
angle_beta	101.20 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.070 Å
resolution_low	20.000 Å
r_factor	0.1840
r_work	0.1840
r_free	0.2310

fit	/app/data/saxs_computation/d4/1d4p/1d4p.fit
pddf	/app/data/pr_computation/d4/1d4p/1d4p.pr.out
profile	/app/data/saxs_computation/d4/1d4p/1d4p.dat

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH 5-AMIDINOINDOLE-4-BENZYLPIPERIDINE INHIBITOR

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)