SAXSdb — 3app

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

PENICILLOPEPSIN

Penicillium janthinellum

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–323	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3APP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1APT CRYSTALLOGRAPHIC ANALYSIS OF A PEPSTATIN ANALOGUE BINDING TO THE ASPARTYL PROTEINASE PENICILLOPEPSIN AT 1.8 ANGSTROMS RESOLUTION Deposited 1991-12-16	Different oligomeric state Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1APU Crystallographic analysis of a pepstatin analogue binding to the aspartyl proteinase penicillopepsin at 1.8 angstroms resolution Deposited 1991-12-16	Different oligomeric state Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1APU Crystallographic analysis of a pepstatin analogue binding to the aspartyl proteinase penicillopepsin at 1.8 angstroms resolution Deposited 1991-12-16	Different oligomeric state Different ligand/ion	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1APV CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES Deposited 1991-12-16	Different oligomeric state Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 XYS alpha-D-xylopyranose × 1 SO4 SULFATE ION × 1 DMF DIMETHYLFORMAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1APW CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES Deposited 1991-12-16	Different oligomeric state Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 HSY alpha-L-xylopyranose × 1 SO4 SULFATE ION × 1 DMF DIMETHYLFORMAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1BXO ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL CYCLO[(2S)-2-[[(1R)-1-(N-(L-N-(3-METHYLBUTANOYL)VALYL-L-ASPARTYL)AMINO)-3-METHYLBUT YL] HYDROXYPHOSPHINYLOXY]-3-(3-AMINOMETHYL) PHENYLPROPANOATE Deposited 1998-10-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 2 SO4 SULFATE ION × 1 PP7 METHYL CYCLO[(2S)-2-[[(1R)-1-(N-(L-N-(3-METHYLBUTANOYL)VALYL-L-ASPARTYL)AMINO)-3-METHYLBUTYL]HYDROXYPHOSPHINYLOXY]-3-(3-AMINOMETHYL)PHENYLPROPANOATE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1 M CH3COONA 35% AMMONIUM SULFATE PH 4.6	Resolution 0.95 Å R-free 0.125
1BXQ ACID PROTEINASE (PENICILLOPEPSIN) COMPLEX WITH PHOSPHONATE INHIBITOR. Deposited 1998-10-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 2 SO4 SULFATE ION × 2 ACT ACETATE ION × 1 PP8 2-[(1R)-1-(N-(3-METHYLBUTANOYL)-L-VALYL-L-ASPARAGINYL)-AMINO)-3-METHYLBUTYL]HYDROXYPHOSPHINYLOXY]-3-PHENYLPROPANOIC ACID METHYLESTER × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1 M CH3COONA 35% SATD. AMMONIUM SULPHATE PH 4.6	Resolution 1.41 Å R-free 0.182
1PPK CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHOROUS-CONTAINING PEPTIDE ANALOGUES Deposited 1994-01-20	Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–323（323 aa）	Not recorded	IVV N-(3-methylbutanoyl)-L-valyl-N-{(1R)-1-[(R)-(2-ethoxy-2-oxoethyl)(hydroxy)phosphoryl]-3-methylbutyl}-L-valinamide × 1 MAN alpha-D-mannopyranose × 1 HSY alpha-L-xylopyranose × 1 SO4 SULFATE ION × 1 DMF DIMETHYLFORMAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1PPL CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES Deposited 1992-06-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–323（323 aa）	Not recorded	1Z7 N-(3-methylbutanoyl)-L-valyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl}-L- valinamide × 1 MAN alpha-D-mannopyranose × 1 XYS alpha-D-xylopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1PPM CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES Deposited 1992-06-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–323（323 aa）	Not recorded	0P1 N-[(benzyloxy)carbonyl]-L-alanyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl }-L-alaninamide × 1 MAN alpha-D-mannopyranose × 1 ARA alpha-L-arabinopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
2WEA ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL[CYCLO-7[(2R)-((N-VALYL) AMINO)-2-(HYDROXYL-(1S)-1-METHYOXYCARBONYL-2-PHENYLETHOXY) PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE], SODIUM SALT Deposited 1998-02-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 4 SO4 SULFATE ION × 2 PP6 METHYL[CYCLO-7[(2R)-((N-VALYL)AMINO)-2-(HYDROXYL-(1S)-1-METHYLOXYCARBONYL-2-PHENYLETHOXY)PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE] × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.4；0.1M NAC2H3O2 PH=4.4 35-40% SATURATED (NH4)2SO4	Resolution 1.25 Å R-free 0.190
2WEB ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL(2S)-[1-(((N-FORMYL)-L-VALYL)AMINO-2-(2-NAPHTHYL)ETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYLPROPANOATE, SODIUM SALT Deposited 1998-02-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 4 SO4 SULFATE ION × 2 PP4 METHYL (2S)-[1-((N-FORMYL)-L-VALYL)AMINO-2-(2-NAPHTHYL)ETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYL PROPANOATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.4；0.1M NAC2H3O2 PH=4.4 35-40% SATURATED (NH4)2SO4	Resolution 1.50 Å R-free 0.190
2WEC ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL(2S)-[1-(((N-(1-NAPHTHALENEACETYL))-L-VALYL)AMINOMETHYL)HYDROXY PHOSPHINYLOXY]-3-PHENYLPROPANOATE, SODIUM SALT Deposited 1998-02-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 4 SO4 SULFATE ION × 2 PP5 METHYL (2S)-[1-((N-(NAPHTHALENEACETYL))-L-VALYL)AMINOMETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYL PROPANOATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.4；0.1M NAC2H3O2 PH=4.4 35-40% SATURATED (NH4)2SO4	Resolution 1.50 Å R-free 0.200
2WED ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE MACROCYCLIC INHIBITOR:METHYL[CYCLO-7[(2R)-((N-VALYL)AMINO)-2-(HYDROXYL-(1S)-1-METHYOXYCARBONYL-2-PHENYLETHOXY)PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE], SODIUM SALT Deposited 1998-02-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–323（323 aa）	Not recorded	MAN alpha-D-mannopyranose × 4 SO4 SULFATE ION × 2 PP6 METHYL[CYCLO-7[(2R)-((N-VALYL)AMINO)-2-(HYDROXYL-(1S)-1-METHYLOXYCARBONYL-2-PHENYLETHOXY)PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE] × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.4；0.1M NAC2H3O2 PH=4.4 35-40% SATURATED (NH4)2SO4	Resolution 1.50 Å R-free 0.190

13 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PENP_PENJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–323； UniProt 1–323

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3app
Deposition date deposition_date	1990-11-27
Structure title title	STRUCTURE AND REFINEMENT OF PENICILLOPEPSIN AT 1.8 ANGSTROMS RESOLUTION
Keywords keywords	HYDROLASE (ACID PROTEINASE); HYDROLASE (ACID PROTEINASE)
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.63 Å
Radius of gyration Rg (electron density) rg_electron	19.35 Å
Forward intensity I(0) i0	20512000.00
Molecular weight molecular_weight	33439.0 kDa
Excluded volume excluded_volume	41234 Å³
Envelope volume envelope_volume	47512 Å³
Hydration-shell volume shell_volume	20574 Å³
Envelope diameter envelope_diameter	65.4 Å
Shell Rg shell_rg	25.68 Å
Envelope Rg envelope_rg	19.39 Å
Shape Rg shape_rg	19.31 Å
Total Rg total_rg	20.26 Å
Total atoms total_atoms	2366
Residues n_residues	323
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	68.5 Å
Rg (real space) rg_real	20.53 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	2.0510e+07
I(0) uncertainty (real space) i0_real_error	2.8840e+05
Rg (reciprocal space) rg_reciprocal	20.55 Å
I(0) (reciprocal space) i0_reciprocal	20510000.0000
Solution quality estimate total_estimate	0.8857
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.194
Kurtosis Kurtosis kurtosis	-0.445
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3894000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3appa_
Class class	b — All beta proteins
Fold Fold fold	b.50 — Acid proteases
Superfamily Superfamily superfamily	b.50.1 — Acid proteases
Family Family family	b.50.1.2 — Pepsin-like

CATH v4.4 (2 domains)

Domain ID domain_id	3appA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

Domain ID domain_id	3appA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

▶

8. Citations (11)

Structure and refinement of penicillopepsin at 1.8 A resolution.

J.Mol.Biol. (1983)

PMID: 6341600 · DOI: 10.1016/0022-2836(83)90008-6 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)

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

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

The Tertiary Structure of Penicillopepsin. Towards a Catalytic Mechanism for Acid Proteases

STRUCTURAL STUDIES ON MOLECULES OF BIOLOGICA INTERESTL (1981)

An X-Ray Crystallographic Approach to Enzyme Structure and Function

Can.J.Biochem. (1980)

Structural Evidence for Gene Duplication in the Evolution of the Acid Proteases

Nature (1978)

Mechanism of Acid Protease Catalysis Based on the Crystal Structure of Penicillopepsin

Nature (1977)

Penicillopepsin from Penicillium Janthinellum Crystal Structure at 2.8 Angstroms and Sequence Homology with Porcine Pepsin

Nature (1977)

Penicillopepsin. 2.8 Angstroms Structure, Active Site Conformation and Mechanistic Implications

Adv.Exp.Med.Biol. (1977)

The Crystal Structure of Penicillopepsin at 6 Angstroms Resolution

Biochem.Biophys.Res.Commun. (1976)

▶

Unit-cell length a length_a	97.370 Å
Unit-cell length b length_b	46.640 Å
Unit-cell length c length_c	65.470 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1260
R_work r_work	—
R_free r_free	—

Description description	PENICILLOPEPSIN
Molecular weight formula_weight	33468.8 kDa
EC 编号 ec_number	3.4.23.20
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2684

STRUCTURE AND REFINEMENT OF PENICILLOPEPSIN AT 1.8 ANGSTROMS RESOLUTION

1. Protein Identity and Related Structures Protein Identity & Related Structures

PENICILLOPEPSIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (11)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Penicillium janthinellum
NCBI Class编号 ncbi_taxonomy_id	5079

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	318

fit	/app/data/saxs_computation/ap/3app/3app.fit
pddf	/app/data/pr_computation/ap/3app/3app.pr.out
profile	/app/data/saxs_computation/ap/3app/3app.dat