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1d8m

CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A HETEROCYCLE-BASED INHIBITOR

Method: X-RAY DIFFRACTION D_max: 82.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d8m
deposition_date	1999-10-25
title	CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A HETEROCYCLE-BASED INHIBITOR
keywords	MIXED ALPHA BETA STRUCTURE, ZINC PROTEASE, INHIBITED, HYDROLASE; HYDROLASE
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	23.62 Å
rg_electron	23.10 Å
i0	26504900.00
molecular_weight	39258.0 kDa
excluded_volume	48896 Å³
envelope_volume	58696 Å³
shell_volume	22186 Å³
envelope_diameter	86.8 Å
shell_rg	29.23 Å
envelope_rg	23.53 Å
shape_rg	23.11 Å
total_rg	23.85 Å
total_atoms	2761
n_residues	342
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	82.0 Å
rg_real	23.80 Å
rg_real_error	0.80 Å
i0_real	2.6500e+07
i0_real_error	3.9920e+05
rg_reciprocal	23.76 Å
i0_reciprocal	26500000.0000
total_estimate	0.7448
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	23.1 Å
skewness	0.588
kurtosis	-0.111
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	10700000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.622; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.815; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	STROMELYSIN-1 PRECURSOR
formula_weight	19416.5 kDa
ec_number	3.4.24.17
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2831

FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPPDSPET

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	1-BENZYL-3-(4-METHOXY-BENZENESULFONYL)-6-OXO-HEXAHYDRO-PYRIMIDINE-4-CARBOXYLIC ACID HYDROXYAMIDE
formula_weight	419.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	70

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6. Citations (1)

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length_a	37.960 Å
length_b	78.590 Å
length_c	105.930 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.440 Å
resolution_low	10.000 Å
r_factor	—
r_work	0.2770
r_free	0.3150

fit	/app/data/saxs_computation/d8/1d8m/1d8m.fit
pddf	/app/data/pr_computation/d8/1d8m/1d8m.pr.out
profile	/app/data/saxs_computation/d8/1d8m/1d8m.dat