SAXSdb — 1pyo

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

Caspase-2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	ACETYL-LEU-ASP-GLU-SER-ASJ × 2 （P36114） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CASP2_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 167–333 Author chain C； PDBConstruct 1–167； UniProt 167–333 Author chain B； PDBConstruct 1–105； UniProt 348–452 Author chain D； PDBConstruct 1–105； UniProt 348–452

ACETYL-LEU-ASP-GLU-SER-ASJ

OrganismNot specified

UniProt P36114

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Caspase-2 × 2 （P42575） Caspase-2 × 2 （P42575） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YKZ8_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 2–6； UniProt 54–58 Author chain F； PDBConstruct 2–6； UniProt 54–58

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	1pyo
Deposition date deposition_date	2003-07-09
Structure title title	Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho
Keywords keywords	APOPTOSIS, CASPASE, ALPHA-BETA, THIOL PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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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.

1pyo__assembly_1__model_1

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

Download this curve (.dat)

1pyo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pyo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.79 Å
Rg (electron density)	22.66 Å
Total Rg	23.45 Å
Atom count	4181
Residues	525
Excluded volume	74176 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pyo__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Caspase-2
Molecular weight formula_weight	18790.3 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4606

NKDGPVCLQVKPCTPEFYQTHFQLAYRLQSRPRGLALVLSNVHFTGEKELEFRSGGDVDHSTLVTLFKLLGYDVHVLCDQTAQEMQEKLQNFAQLPAHRVTDSCIVALLSHGVEGAIYGVDGKLLQLQEVFQLFDNANCPSLQNKPKMFFIQACRGDETDRGVDQQD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Caspase-2
Molecular weight formula_weight	11921.0 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

AGKEKLPKMRLPTRSDMICGYACLKGTAAMRNTKRGSWYIEALAQVFSERACDMHVADMLVKVNALIKDREGYAPGTEFHRCKEMSEYCSTLCRHLYLFPGHPPT

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	ACETYL-LEU-ASP-GLU-SER-ASJ
Molecular weight formula_weight	589.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

XLDESX

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	385

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1pyo.1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.17 — Caspase-like
Superfamily Superfamily superfamily	c.17.1 — Caspase-like
Family Family family	c.17.1.1 — Caspase catalytic domain

Domain ID domain_id	d1pyo.2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.17 — Caspase-like
Superfamily Superfamily superfamily	c.17.1 — Caspase-like
Family Family family	c.17.1.1 — Caspase catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1pyoA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1460 —

Domain ID domain_id	1pyoB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1470 — Caspase-like

Domain ID domain_id	1pyoC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1460 —

Domain ID domain_id	1pyoD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1470 — Caspase-like

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Unit-cell length a length_a	63.649 Å
Unit-cell length b length_b	96.583 Å
Unit-cell length c length_c	97.547 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1890
R_free r_free	0.2130

Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho

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

Caspase-2

State in the Current Structure

Other States of the Same Protein in the Database

ACETYL-LEU-ASP-GLU-SER-ASJ

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

1pyo__assembly_1__model_1

1pyo__assembly_1__model_1 | I(q)

1pyo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho

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

Caspase-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ACETYL-LEU-ASP-GLU-SER-ASJ

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

1pyo__assembly_1__model_1

1pyo__assembly_1__model_1 | I(q)

1pyo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)