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1apv

;CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES ;

Method: X-RAY DIFFRACTION D_max: 64.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1apv
deposition_date	1991-12-16
title	;CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES ;
keywords	ACID PROTEINASE, 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	20.57 Å
rg_electron	19.25 Å
i0	21592400.00
molecular_weight	34429.0 kDa
excluded_volume	42478 Å³
envelope_volume	48004 Å³
shell_volume	20803 Å³
envelope_diameter	66.8 Å
shell_rg	25.71 Å
envelope_rg	19.42 Å
shape_rg	19.22 Å
total_rg	20.16 Å
total_atoms	2432
n_residues	325
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	64.3 Å
rg_real	20.48 Å
rg_real_error	0.30 Å
i0_real	2.1590e+07
i0_real_error	2.6510e+05
rg_reciprocal	20.50 Å
i0_reciprocal	21590000.0000
total_estimate	0.9018
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.1 Å
skewness	0.212
kurtosis	-0.432
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	4432000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	PENICILLOPEPSIN
formula_weight	33468.8 kDa
ec_number	3.4.23.20
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E
atom_count	2709

AASGVATNTPTANDEEYITPVTIGGTTLNLNFDTGSADLWVFSTELPASQQSGHSVYNPSATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQDTNNDGLLGLAFSSINTVQPQSQTTFFDTVKSSLAQPLFAVALKHQQPGVYDFGFIDSSKYTGSLTYTGVDNSQGFWSFNVDSYTAGSQSGDGFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGGIQSNSGIGFSIFGDIFLKSQYVVFDSDGPQLGFAPQA

Source

organism	Penicillium janthinellum
common_name	Penicillium vitale
ncbi_taxonomy_id	5079

Entity 2 polymer

description	INHIBITOR ISOVALERYL (IVA)-VAL-VAL-HYDRATED DIFLUOROSTATONE-N-METHYLAMINE
formula_weight	522.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

XVVXX

Entity 3 non-polymer

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

Entity 4 non-polymer

description	alpha-D-xylopyranose
formula_weight	150.1 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	DIMETHYLFORMAMIDE
formula_weight	73.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	277

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6. Citations (8)

;Crystallographic analysis of transition state mimics bound to penicillopepsin: difluorostatine- and difluorostatone-containing peptides. ;

Biochemistry (1992)

PMID: 1567842 · DOI: 10.1021/bi00130a019 PRIMARY

Aspartic Proteinases and Their Catalytic Pathway

Biological Macromolecules and Assemblies (1987)

Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin

Biochemistry (1985)

X-Ray Diffraction Studies on Penicillopepsin and its Complexes: The Hydrolytic Mechanism

Aspartic Proteinases and Their Inhibitors (1985)

;Effect of Ph on the Activities of Penicillopepsin and Rhizopus Pepsin and a Proposal for the Productive Substrate Binding Mode in Penicillopepsin ;

Biochemistry (1984)

Crystallographic Analysis of a Pepstatin Analogue Binding to the Aspartyl Proteinase Penicillopepsin at 1.8 Angstroms Resolution

Peptides: Structure and Function, Proceedings of the of the Eighth American Peptide Symposium (1983)

Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution

J.Mol.Biol. (1983)

Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin

Proc.Natl.Acad.Sci.USA (1982)

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length_a	97.520 Å
length_b	46.570 Å
length_c	66.230 Å
angle_alpha	90.00 °
angle_beta	116.03 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.800 Å
resolution_low	8.000 Å
r_factor	0.1310
r_work	—
r_free	—

fit	/app/data/saxs_computation/ap/1apv/1apv.fit
pddf	/app/data/pr_computation/ap/1apv/1apv.pr.out
profile	/app/data/saxs_computation/ap/1apv/1apv.dat

;CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES ;

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (8)

7. Files & Curves (10)

Files (7)

Curves (3)