SAXSdb — 4az3

▼

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

LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAIN

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;(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 CADMIUM ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPGB_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 3–300； UniProt 29–326 Author chain B； PDBConstruct 1–154； UniProt 327–480

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4az3
Deposition date deposition_date	2012-06-22
Structure title title	crystal structure of cathepsin a, complexed with 15a
Keywords keywords	HYDROLASE, DRUG DISCOVERY, CARBOXYPEPTIDASE, CARDIOVASCULAR; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4az3__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4az3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4az3__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.59 Å
Rg (electron density)	21.36 Å
Total Rg	22.47 Å
Atom count	3383
Residues	414
Excluded volume	60125 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4az3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAIN
Molecular weight formula_weight	33773.7 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	3854

SRAPDQDEIQRLPGLAKQPSFRQYSGYLKGSGSKHLHYWFVESQKDPENSPVVLWLNGGPGCSSLDGLLTEHGPFLVQPDGVTLEYNPYSWNLIANVLYLESPAGVGFSYSDDKFYATNDTEVAQSNFEALQDFFRLFPEYKNNKLFLTGESYAGIYIPTLAVLVMQDPSMNLQGLAVGNGLSSYEQNDNSLVYFAYYHGLLGNRLWSSLQTHCCSQNKCNFYDNKDLECVTNLQEVARIVGNSGLNIYNLYAPCAGGVPSHFRYEKDTVVVQDLGNIFTRLPLKRMWHQALLRSGDKVR

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	SPODOPTERA FRUGIPERDA

Entity 2 Entity 2 polymer

Description description	LYSOSOMAL PROTECTIVE PROTEIN 20 KDA CHAIN
Molecular weight formula_weight	18073.7 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	B

MDPPCTNTTAASTYLNNPYVRKALNIPEQLPQWDMCNFLVNLQYRRLYRSMNSQYLKLLSSQKYQILLYNGDVDMACNFMGDEWFVDSLNQKMEVQRRPWLVKYGDSGEQIAGFVKEFSHIAFLTIKGAGHMVPTDKPLAAFTMFSRFLNKQPYE

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	SPODOPTERA FRUGIPERDA

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	;(3S)-3-({[1-(2-fluorophenyl)-5-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-1H-pyrazol-3-yl]carbonyl}amino)-3-(2-methylphenyl)propanoic acid ;
Molecular weight formula_weight	483.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	422

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4az3A00
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

Domain ID domain_id	4az3B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12670 —

▶

Unit-cell length a length_a	90.590 Å
Unit-cell length b length_b	102.800 Å
Unit-cell length c length_c	48.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.87 °
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	2.040 Å
Low-resolution limit resolution_low	47.360 Å
R factor r_factor	—
R_work r_work	0.1880
R_free r_free	0.2150

crystal structure of cathepsin a, complexed with 15a

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

LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4az3__assembly_1__model_1

4az3__assembly_1__model_1 | I(q)

4az3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

crystal structure of cathepsin a, complexed with 15a

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

LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4az3__assembly_1__model_1

4az3__assembly_1__model_1 | I(q)

4az3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)