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1dva

Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor VIIA

Method: X-RAY DIFFRACTION D_max: 96.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dva
deposition_date	2000-01-20
title	Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor VIIA
keywords	protein-peptide complex, 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	30.39 Å
rg_electron	29.73 Å
i0	228732000.00
molecular_weight	78924.0 kDa
excluded_volume	75389 Å³
envelope_volume	133110 Å³
shell_volume	37615 Å³
envelope_diameter	102.8 Å
shell_rg	36.78 Å
envelope_rg	29.40 Å
shape_rg	29.68 Å
total_rg	30.28 Å
total_atoms	5913
n_residues	746
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	96.6 Å
rg_real	30.36 Å
rg_real_error	0.63 Å
i0_real	2.2870e+08
i0_real_error	3.4890e+06
rg_reciprocal	30.38 Å
i0_reciprocal	228700000.0000
total_estimate	0.9029
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.4 Å
skewness	0.284
kurtosis	-0.517
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	15240000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.943

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	DES-GLA FACTOR VIIA (HEAVY CHAIN)
formula_weight	28103.3 kDa
ec_number	3.4.21.21
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,I
atom_count	5917

IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	DES-GLA FACTOR VIIA (LIGHT CHAIN)
formula_weight	10994.2 kDa
ec_number	3.4.21.21
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,M

ISYSDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	PEPTIDE E-76
formula_weight	2198.5 kDa
src_method	syn
entity_count	2

Polymer

type	polypeptide(L)
strand_id	X,Y

XALCDDPRVDRWYCQFVEGX

Entity 4 branched

description	beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
formula_weight	342.3 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide
formula_weight	504.0 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	CACODYLATE ION
formula_weight	137.0 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	alpha-L-fucopyranose
formula_weight	164.2 kDa
src_method	man
entity_count	2

Entity 9 non-polymer

description	alpha-D-glucopyranose
formula_weight	180.2 kDa
src_method	man
entity_count	1

Entity 10 non-polymer

description	beta-L-fucopyranose
formula_weight	164.2 kDa
src_method	man
entity_count	1

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

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6. Citations (1)

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length_a	70.490 Å
length_b	55.260 Å
length_c	111.730 Å
angle_alpha	90.00 °
angle_beta	99.48 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	3.000 Å
resolution_low	50.000 Å
r_factor	0.2280
r_work	0.2250
r_free	0.2950

fit	/app/data/saxs_computation/dv/1dva/1dva.fit
pddf	/app/data/pr_computation/dv/1dva/1dva.pr.out
profile	/app/data/saxs_computation/dv/1dva/1dva.dat

Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor VIIA

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 (11)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)