SAXSdb — 1lyw

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

CATHEPSIN D

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 4	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 water × 4	Consistent with protein count
11	Protein homooligomer	Homooligomer	Protein 4	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 water × 4	Consistent with protein count
12	Protein homooligomer	Homooligomer	Protein 4	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 8	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 4 water × 8	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 8	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 4 water × 8	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 4	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 water × 4	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 4	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 water × 4	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 4	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CATD_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 65–161 Author chain C； PDBConstruct 1–97； UniProt 65–161 Author chain E； PDBConstruct 1–97； UniProt 65–161 Author chain G； PDBConstruct 1–97； UniProt 65–161 Author chain B； PDBConstruct 1–241； UniProt 170–410 Author chain D； PDBConstruct 1–241； UniProt 170–410 Author chain F； PDBConstruct 1–241； UniProt 170–410 Author chain H； PDBConstruct 1–241； UniProt 170–410

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	1lyw
Deposition date deposition_date	1998-06-30
Structure title title	CATHEPSIN D AT PH 7.5
Keywords keywords	ASPARTIC PROTEASE, HYDROLASE, GLYCOPROTEIN; ASPARTIC PROTEASE
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.

1lyw__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1lyw__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1lyw__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	21.12 Å
Rg (electron density)	20.04 Å
Total Rg	21.04 Å
Atom count	3142
Residues	336
Excluded volume	46543 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1lyw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1lyw__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1lyw__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1lyw__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1lyw__assembly_5__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1lyw__assembly_6__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1lyw__assembly_7__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`1lyw__assembly_8__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`1lyw__assembly_9__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`1lyw__assembly_10__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`1lyw__assembly_11__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`1lyw__assembly_12__model_1`	tetrameric （4）	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	CATHEPSIN D
Molecular weight formula_weight	10688.9 kDa
EC 编号 ec_number	3.4.23.5
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	14242

GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQ

Entity 2 Entity 2 polymer

Description description	CATHEPSIN D
Molecular weight formula_weight	26270.2 kDa
EC 编号 ec_number	3.4.23.5
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

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

GGVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	558

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1lyw.1
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

Domain ID domain_id	d1lyw.2
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

Domain ID domain_id	d1lyw.3
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

Domain ID domain_id	d1lyw.4
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 (8 domains)

Domain ID domain_id	1lywA00
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	1lywB00
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	1lywC00
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	1lywD00
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	1lywE00
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	1lywF00
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	1lywG00
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	1lywH00
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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Unit-cell length a length_a	140.256 Å
Unit-cell length b length_b	136.797 Å
Unit-cell length c length_c	140.416 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2570

CATHEPSIN D AT PH 7.5

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

CATHEPSIN D

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

1lyw__assembly_4__model_1

1lyw__assembly_4__model_1 | I(q)

1lyw__assembly_4__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (3)

CATHEPSIN D AT PH 7.5

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

CATHEPSIN D

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

1lyw__assembly_4__model_1

1lyw__assembly_4__model_1 | I(q)

1lyw__assembly_4__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (3)