SAXSdb — 1bxq

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

PROTEIN (PENICILLOPEPSIN)

OrganismNot specified

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	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

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 1BXQ	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 Different experimental conditions Different structure-quality metrics	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 Different experimental conditions Different structure-quality metrics	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 Different experimental conditions Different structure-quality metrics	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 Different experimental conditions Different structure-quality metrics	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 Different experimental conditions Different structure-quality metrics	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
1PPK CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHOROUS-CONTAINING PEPTIDE ANALOGUES Deposited 1994-01-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	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 experimental conditions 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 experimental conditions 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 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	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 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bxq
Deposition date deposition_date	1998-10-07
Structure title title	ACID PROTEINASE (PENICILLOPEPSIN) COMPLEX WITH PHOSPHONATE INHIBITOR.
Keywords keywords	HYDROLASE, PHOSPHONATE INHIBITORS; HYDROLASE
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	20.51 Å
Radius of gyration Rg (electron density) rg_electron	19.18 Å
Forward intensity I(0) i0	22538000.00
Molecular weight molecular_weight	34919.0 kDa
Excluded volume excluded_volume	42985 Å³
Envelope volume envelope_volume	48334 Å³
Hydration-shell volume shell_volume	20897 Å³
Envelope diameter envelope_diameter	65.0 Å
Shell Rg shell_rg	25.82 Å
Envelope Rg envelope_rg	19.46 Å
Shape Rg shape_rg	19.14 Å
Total Rg total_rg	20.14 Å
Total atoms total_atoms	2463
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	65.5 Å
Rg (real space) rg_real	20.42 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	2.2540e+07
I(0) uncertainty (real space) i0_real_error	2.6680e+05
Rg (reciprocal space) rg_reciprocal	20.44 Å
I(0) (reciprocal space) i0_reciprocal	22540000.0000
Solution quality estimate total_estimate	0.8965
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.216
Kurtosis Kurtosis kurtosis	-0.421
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4835000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 1.000

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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	PROTEIN (PENICILLOPEPSIN)
Molecular weight formula_weight	33468.8 kDa
EC 编号 ec_number	3.4.23.20
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2894

AASGVATNTPTANDEEYITPVTIGGTTLNLNFDTGSADLWVFSTELPASQQSGHSVYNPSATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQDTNNDGLLGLAFSSINTVQPQSQTTFFDTVKSSLAQPLFAVALKHQQPGVYDFGFIDSSKYTGSLTYTGVDNSQGFWSFNVDSYTAGSQSGDGFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGGIQSNSGIGFSIFGDIFLKSQYVVFDSDGPQLGFAPQA

Entity 2 Entity 2 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	;2-[(1R)-1-(N-(3-METHYLBUTANOYL)-L-VALYL-L-ASPARAGINYL)-AMINO)-3-METHYLBUTYL]HYDROXYPHOSPHINYLOXY]-3-PHENYLPROPANOIC ACID METHYLESTER ;
Molecular weight formula_weight	626.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	405

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bxqa_
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	1bxqA01
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	1bxqA02
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 (3)

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Unit-cell length a length_a	95.829 Å
Unit-cell length b length_b	46.431 Å
Unit-cell length c length_c	65.186 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.39 °
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	1.410 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1431
R_work r_work	—
R_free r_free	0.1821

fit	/app/data/saxs_computation/bx/1bxq/1bxq.fit
pddf	/app/data/pr_computation/bx/1bxq/1bxq.pr.out
profile	/app/data/saxs_computation/bx/1bxq/1bxq.dat

ACID PROTEINASE (PENICILLOPEPSIN) COMPLEX WITH PHOSPHONATE INHIBITOR.