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1c1v

RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES

Method: X-RAY DIFFRACTION D_max: 59.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1c1v
deposition_date	1999-07-21
title	RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES
keywords	;ZN(II)-MEDIATED SERINE PROTEASE INHIBITORS, PH DEPENDENCE, ZN(II) AFFINITY STUCTURE-BASED DRUG DESIGN, SERINE PROTEASE/INHIBITOR, 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	19.37 Å
rg_electron	18.13 Å
i0	21636200.00
molecular_weight	35051.0 kDa
excluded_volume	43648 Å³
envelope_volume	48862 Å³
shell_volume	21600 Å³
envelope_diameter	61.2 Å
shell_rg	25.39 Å
envelope_rg	18.51 Å
shape_rg	18.13 Å
total_rg	19.10 Å
total_atoms	4850
n_residues	298
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	59.8 Å
rg_real	19.20 Å
rg_real_error	0.22 Å
i0_real	2.1640e+07
i0_real_error	2.3510e+05
rg_reciprocal	19.23 Å
i0_reciprocal	21640000.0000
total_estimate	0.8947
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.3 Å
skewness	0.103
kurtosis	-0.431
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0001
highest_alpha	8682000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Thrombin light chain
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	5639

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

description	Thrombin heavy chain
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-2
formula_weight	1491.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

DFEEIPEEYLQ

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE
formula_weight	335.4 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	263

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6. Citations (1)

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7. Files & Curves (10)

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8. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

domain_id	d1c1v.1
class	b — All beta proteins
fold	b.47 — Trypsin-like serine proteases
superfamily	b.47.1 — Trypsin-like serine proteases
family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (2 domains)

domain_id	1c1vH01
class	2 — Mainly Beta
architecture	40 — Beta Barrel
topology	10 — Thrombin, subunit H
homologous superfamily	10 — Trypsin-like serine proteases

domain_id	1c1vH02
class	2 — Mainly Beta
architecture	40 — Beta Barrel
topology	10 — Thrombin, subunit H
homologous superfamily	10 — Trypsin-like serine proteases

length_a	72.470 Å
length_b	72.090 Å
length_c	73.110 Å
angle_alpha	90.00 °
angle_beta	101.51 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.980 Å
resolution_low	7.500 Å
r_factor	0.2040
r_work	0.2040
r_free	0.2480

fit	/app/data/saxs_computation/c1/1c1v/1c1v.fit
pddf	/app/data/pr_computation/c1/1c1v/1c1v.pr.out
profile	/app/data/saxs_computation/c1/1c1v/1c1v.dat

RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES

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

Entity 2 polymer

Polymer

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)

8. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)