SAXSdb — 1ppk

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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 E； UniProt 1–323	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 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 1PPK	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
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
3APP STRUCTURE AND REFINEMENT OF PENICILLOPEPSIN AT 1.8 ANGSTROMS RESOLUTION Deposited 1990-11-27	Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–323（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å

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 E； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ppk
Deposition date deposition_date	1994-01-20
Structure title title	CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHOROUS-CONTAINING PEPTIDE ANALOGUES
Keywords keywords	ACID PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	20.58 Å
Radius of gyration Rg (electron density) rg_electron	19.25 Å
Forward intensity I(0) i0	21656400.00
Molecular weight molecular_weight	34424.0 kDa
Excluded volume excluded_volume	42463 Å³
Envelope volume envelope_volume	47867 Å³
Hydration-shell volume shell_volume	20760 Å³
Envelope diameter envelope_diameter	67.2 Å
Shell Rg shell_rg	25.79 Å
Envelope Rg envelope_rg	19.42 Å
Shape Rg shape_rg	19.22 Å
Total Rg total_rg	20.18 Å
Total atoms total_atoms	2431
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

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

Maximum dimension Dmax dmax	66.7 Å
Rg (real space) rg_real	20.49 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.1660e+07
I(0) uncertainty (real space) i0_real_error	2.5770e+05
Rg (reciprocal space) rg_reciprocal	20.51 Å
I(0) (reciprocal space) i0_reciprocal	21660000.0000
Solution quality estimate total_estimate	0.8157
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.218
Kurtosis Kurtosis kurtosis	-0.425
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4614000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

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 Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	2706

AASGVATNTPTANDEEYITPVTIGGTTLNLNFDTGSADLWVFSTELPASQQSGHSVYNPSATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQDTNNDGLLGLAFSSINTVQPQSQTTFFDTVKSSLAQPLFAVALKHQQPGVYDFGFIDSSKYTGSLTYTGVDNSQGFWSFNVDSYTAGSQSGDGFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGGIQSNSGIGFSIFGDIFLKSQYVVFDSDGPQLGFAPQA

来源 Source

来源生物 organism	Penicillium janthinellum
NCBI Class编号 ncbi_taxonomy_id	5079

Entity 2 Entity 2 non-polymer

Description description	N-(3-methylbutanoyl)-L-valyl-N-{(1R)-1-[(R)-(2-ethoxy-2-oxoethyl)(hydroxy)phosphoryl]-3-methylbutyl}-L-valinamide
Molecular weight formula_weight	519.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	alpha-L-xylopyranose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	DIMETHYLFORMAMIDE
Molecular weight formula_weight	73.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	275

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ppke_
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	1ppkE01
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	1ppkE02
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

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8. Citations (9)

Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues.

Biochemistry (1992)

PMID: 1606144 · DOI: 10.1021/bi00137a016 PRIMARY

;Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Difluorostatine-and Difluorostatone-Containing Peptides ;

Biochemistry (1992)

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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Unit-cell length a length_a	97.480 Å
Unit-cell length b length_b	46.550 Å
Unit-cell length c length_c	66.420 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.14 °
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	0.1320
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/pp/1ppk/1ppk.fit
pddf	/app/data/pr_computation/pp/1ppk/1ppk.pr.out
profile	/app/data/saxs_computation/pp/1ppk/1ppk.dat

CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHOROUS-CONTAINING PEPTIDE ANALOGUES