← Back to search

1db4

HUMAN S-PLA2 IN COMPLEX WITH INDOLE 8

Method: X-RAY DIFFRACTION D_max: 54.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1db4
deposition_date	1999-11-02
title	HUMAN S-PLA2 IN COMPLEX WITH INDOLE 8
keywords	S-PLA2, STRUCTURE-BASED DRUG DESIGN, HYDROLASE/HYDROLASE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	15.21 Å
rg_electron	14.26 Å
i0	4749740.00
molecular_weight	14430.0 kDa
excluded_volume	17564 Å³
envelope_volume	19682 Å³
shell_volume	11887 Å³
envelope_diameter	52.5 Å
shell_rg	19.86 Å
envelope_rg	14.66 Å
shape_rg	14.25 Å
total_rg	15.37 Å
total_atoms	997
n_residues	124
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

▼

3. P(r) Analysis (GNOM)

dmax	54.3 Å
rg_real	15.17 Å
rg_real_error	0.33 Å
i0_real	4.7500e+06
i0_real_error	4.7270e+04
rg_reciprocal	15.18 Å
i0_reciprocal	4750000.0000
total_estimate	0.8501
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.6 Å
skewness	0.283
kurtosis	-0.320
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	1256000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.709; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.997

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	PHOSPHOLIPASE A2
formula_weight	13945.0 kDa
ec_number	3.1.1.4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1066

NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	[3-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-PROPYL-]-PHOSPHONIC ACID
formula_weight	416.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	69

▶

6. Citations (1)

▶

length_a	77.012 Å
length_b	77.012 Å
length_c	91.620 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	2.200 Å
resolution_low	30.000 Å
r_factor	0.2260
r_work	0.2260
r_free	0.2560

fit	/app/data/saxs_computation/db/1db4/1db4.fit
pddf	/app/data/pr_computation/db/1db4/1db4.pr.out
profile	/app/data/saxs_computation/db/1db4/1db4.dat

HUMAN S-PLA2 IN COMPLEX WITH INDOLE 8

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