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1dwc

CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS

Method: X-RAY DIFFRACTION D_max: 59.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dwc
deposition_date	1992-08-19
title	CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS
keywords	SERINE PROTEINASE, HYDROLASE-HYROLASE INHIBITOR COMPLEX; HYDROLASE/HYROLASE 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	19.29 Å
rg_electron	18.11 Å
i0	19930200.00
molecular_weight	34006.0 kDa
excluded_volume	42571 Å³
envelope_volume	48376 Å³
shell_volume	21440 Å³
envelope_diameter	60.2 Å
shell_rg	25.26 Å
envelope_rg	18.45 Å
shape_rg	18.10 Å
total_rg	19.12 Å
total_atoms	2386
n_residues	297
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	59.2 Å
rg_real	19.13 Å
rg_real_error	0.21 Å
i0_real	1.9930e+07
i0_real_error	2.3360e+05
rg_reciprocal	19.15 Å
i0_reciprocal	19930000.0000
total_estimate	0.8974
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.0 Å
skewness	0.077
kurtosis	-0.471
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	8169000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	ALPHA-THROMBIN (SMALL SUBUNIT)
formula_weight	4096.5 kDa
ec_number	3.4.21.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L
atom_count	2437

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 2 polymer

description	ALPHA-THROMBIN (LARGE SUBUNIT)
formula_weight	29780.2 kDa
ec_number	3.4.21.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 3 polymer

description	HIRUDIN IIIA
formula_weight	1411.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

DFEEIPEEYLQ

Source

organism	Hirudo medicinalis
common_name	medicinal leech
ncbi_taxonomy_id	6421

Entity 4 non-polymer

description	;amino{[(4S)-5-[(2R,4R)-2-carboxy-4-methylpiperidin-1-yl]-4-({[(3R)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}amino)-5-oxopentyl]amino}methaniminium ;
formula_weight	509.6 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	50

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6. Citations (7)

Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors.

J.Biol.Chem. (1991)

PMID: 1939071 PRIMARY

;The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships. ;

Protein Sci. (1992)

PMID: 1304349

The interaction of thrombin with fibrinogen. A structural basis for its specificity.

Eur.J.Biochem. (1992)

PMID: 1587268

;Geometry of binding of the benzamidine- and arginine-based inhibitors N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-pipe ridine (NAPAP) and (2R,4R)-4-methyl-1-[N alpha-(3-methyl-1,2,3,4-tetrahydro-8- quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (MQPA) to human alpha-thrombin. X-ray crystallographic determination of the NAPAP-trypsin complex and modeling of NAPAP-thrombin and MQPA-thrombin. ;

Eur.J.Biochem. (1990)

PMID: 2226434

The structure of a complex of recombinant hirudin and human alpha-thrombin.

Science (1990)

PMID: 2374926

Crystal structure of the thrombin-hirudin complex: a novel mode of serine protease inhibition.

Embo J. (1990)

PMID: 2369893

;The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment. ;

Embo J. (1989)

PMID: 2583108

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length_a	90.800 Å
length_b	90.800 Å
length_c	132.500 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	3.000 Å
resolution_low	25.000 Å
r_factor	0.1500
r_work	—
r_free	—

fit	/app/data/saxs_computation/dw/1dwc/1dwc.fit
pddf	/app/data/pr_computation/dw/1dwc/1dwc.pr.out
profile	/app/data/saxs_computation/dw/1dwc/1dwc.dat

CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (7)

7. Files & Curves (10)

Files (7)

Curves (3)