SAXSdb — 4cia

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

LYSOSOMAL PROTECTIVE PROTEIN

HOMO SAPIENS

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 29–480	Not recorded	6KZ N-[(2S)-4-methyl-1-oxidanylidene-1-[[(1R,2S)-1-oxidanyl-1-(5-phenyl-1,2,4-oxadiazol-3-yl)butan-2-yl]amino]pentan-2-yl]morpholine-4-carboxamide × 2 CD CADMIUM ION × 14 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATHEPSIN A WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4DEG.C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	Resolution 1.98 Å R-free 0.232

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 4CIA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IVY PHYSIOLOGICAL DIMER HPP PRECURSOR Deposited 1996-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–480（452 aa） Chain B 29–480（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；285 K；PEG 8000, PH 8.0 - 8.3 AT 4 - 12 DEGREES CELSIUS, temperature 285K	Resolution 2.20 Å R-free 0.268
3BP4 The high resolution crystal structure of HLA-B*2705 in complex with a Cathepsin A signal sequence peptide pCatA Deposited 2007-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–10（9 aa） Fragment：Cathepsin A signal sequence, UNP residues 2-10	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；23% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.222
3BP7 The high resolution crystal structure of HLA-B*2709 in complex with a Cathepsin A signal sequence peptide, pCatA Deposited 2007-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–10（9 aa） Fragment：Cathepsin A signal sequence, UNP residues 2-10	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；23.5% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.204
3BXN The high resolution crystal structure of HLA-B*1402 complexed with a Cathepsin A signal sequence peptide, pCatA Deposited 2008-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–10（9 aa） Fragment：signal sequence peptide, residues 2-10	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；24- 27%(w/v) PEG 20000, with 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.86 Å R-free 0.219
4AZ0 crystal structure of cathepsin a, complexed with 8a. Deposited 2012-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 29–326（298 aa） Chain B 327–480（154 aa）	Not recorded	S61 (S)-3-{[1-(2-Fluoro-phenyl)-5-hydroxy-1H-pyrazole-3-carbonyl]-amino}-3-o-tolyl-propionic acid × 2 CD CADMIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATA WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4 DEG. C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	Resolution 2.17 Å
4AZ3 crystal structure of cathepsin a, complexed with 15a Deposited 2012-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–326（298 aa） Fragment：ACTIVATED PROTEASE RESIDUES 29-326 Chain B 327–480（154 aa） Fragment：ACTIVATED PROTEASE, RESIDUES 327-480	Not recorded	S35 (3S)-3-({[1-(2-fluorophenyl)-5-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-1H-pyrazol-3-yl]carbonyl}amino)-3-(2-methylphenyl)propanoic acid × 1 CD CADMIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATA WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4 DEG. C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	Resolution 2.04 Å R-free 0.215
4CI9 Crystal structure of cathepsin A, apo-structure Deposited 2013-12-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–480（452 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 2 ACT ACETATE ION × 4 GOL GLYCEROL × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATHEPSIN A WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4DEG.C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	Resolution 1.58 Å R-free 0.191
4CIB crystal structure of cathepsin a, complexed with compound 2 Deposited 2013-12-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–480（452 aa）	Not recorded	7UZ 2-(cyclohexylmethyl)propanedioic acid × 2 CD CADMIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATHEPSIN A WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4DEG.C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	Resolution 1.89 Å R-free 0.211
4MWS Crystal structure of human PPCA (trigonal crystal form 1) Deposited 2013-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–480（452 aa） Chain B 29–480（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；10% PEG 3350, 0.1M sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.195
4MWT Crystal structure of human PPCA (trigonal crystal form 2) Deposited 2013-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–480（452 aa） Chain B 29–480（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；10% PEG 3350, 0.1M ammonium tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.85 Å R-free 0.325
6WIA CRYSTAL STRUCTURE OF HUMAN PROTECTIVE PROTEIN/CATHEPSIN A, DFP-INHIBITED (AGED) Deposited 2020-04-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–480（452 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 10 CD CADMIUM ION × 12 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；Crystallized in Crystal Screen Cryo II condition #12 (0.095 M cadmium chloride hydrate, 0.095 M sodium acetate trihydrate pH 4.6, 28.5% v/v PEG 400, 5% glycerol). Mounted in 30% glycerol and 70% CS Cryo II condition #12. Protein was inhibited with DFP in 25 mM Tris pH 8, 300 mM NaCl at R.T.	Resolution 2.21 Å R-free 0.224

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPGB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–454； UniProt 29–480

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	4cia
Deposition date deposition_date	2013-12-06
Structure title title	Crystal structure of cathepsin A, complexed with compound 1
Keywords keywords	HYDROLASE, SERINE CARBOXYPEPTIDASE, CARDIOVASCULAR DRUG, HEART FAILURE, ENDOTHELIN, TETRAHEDRAL INTERMEDIATE, COVALENT INHIBITOR; 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	22.31 Å
Radius of gyration Rg (electron density) rg_electron	21.11 Å
Forward intensity I(0) i0	39622600.00
Molecular weight molecular_weight	48047.0 kDa
Excluded volume excluded_volume	59442 Å³
Envelope volume envelope_volume	67683 Å³
Hydration-shell volume shell_volume	26052 Å³
Envelope diameter envelope_diameter	75.4 Å
Shell Rg shell_rg	28.74 Å
Envelope Rg envelope_rg	21.44 Å
Shape Rg shape_rg	21.04 Å
Total Rg total_rg	22.19 Å
Total atoms total_atoms	3341
Residues n_residues	413
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	72.5 Å
Rg (real space) rg_real	22.22 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	3.9620e+07
I(0) uncertainty (real space) i0_real_error	4.4280e+05
Rg (reciprocal space) rg_reciprocal	22.24 Å
I(0) (reciprocal space) i0_reciprocal	39620000.0000
Solution quality estimate total_estimate	0.6980
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.6 Å
Skewness Skewness skewness	0.276
Kurtosis Kurtosis kurtosis	-0.237
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7606000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 0.189; Positv: 1.000; Valcen: 0.995; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	LYSOSOMAL PROTECTIVE PROTEIN
Molecular weight formula_weight	51829.4 kDa
EC 编号 ec_number	3.4.16.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3710

SRAPDQDEIQRLPGLAKQPSFRQYSGYLKGSGSKHLHYWFVESQKDPENSPVVLWLNGGPGCSSLDGLLTEHGPFLVQPDGVTLEYNPYSWNLIANVLYLESPAGVGFSYSDDKFYATNDTEVAQSNFEALQDFFRLFPEYKNNKLFLTGESYAGIYIPTLAVLVMQDPSMNLQGLAVGNGLSSYEQNDNSLVYFAYYHGLLGNRLWSSLQTHCCSQNKCNFYDNKDLECVTNLQEVARIVGNSGLNIYNLYAPCAGGVPSHFRYEKDTVVVQDLGNIFTRLPLKRMWHQALLRSGDKVRMDPPCTNTTAASTYLNNPYVRKALNIPEQLPQWDMCNFLVNLQYRRLYRSMNSQYLKLLSSQKYQILLYNGDVDMACNFMGDEWFVDSLNQKMEVQRRPWLVKYGDSGEQIAGFVKEFSHIAFLTIKGAGHMVPTDKPLAAFTMFSRFLNKQPYE

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	SPODOPTERA FRUGIPERDA

Entity 2 Entity 2 non-polymer

Description description	;N-[(2S)-4-methyl-1-oxidanylidene-1-[[(1R,2S)-1-oxidanyl-1-(5-phenyl-1,2,4-oxadiazol-3-yl)butan-2-yl]amino]pentan-2-yl]morpholine-4-carboxamide ;
Molecular weight formula_weight	459.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	358

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4ciaa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.5 — Serine carboxypeptidase-like

Domain ID domain_id	d4ciaa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ciaa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	4ciaA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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8. Citations (2)

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Unit-cell length a length_a	90.106 Å
Unit-cell length b length_b	101.295 Å
Unit-cell length c length_c	48.077 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.91 °
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	1.980 Å
Low-resolution limit resolution_low	36.110 Å
R factor r_factor	0.1729
R_work r_work	0.1699
R_free r_free	0.2320

fit	/app/data/saxs_computation/ci/4cia/4cia.fit
pddf	/app/data/pr_computation/ci/4cia/4cia.pr.out
profile	/app/data/saxs_computation/ci/4cia/4cia.dat

Crystal structure of cathepsin A, complexed with compound 1

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

LYSOSOMAL PROTECTIVE PROTEIN

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

Diffraction experiment Diffraction