SAXSdb — 1sp4

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

Cathepsin B

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	;methyl N-[(2S)-4-{[(1S)-1-{[(2S)-2-carboxypyrrolidin-1-yl]carbonyl}-3-methylbutyl]amino}-2-hydroxy-4-oxobutanoyl]-L-leucylglycylglycinate ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CATB_BOVIN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–48； UniProt 80–127 Author chain B； PDBConstruct 1–205； UniProt 128–332

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	1sp4
Deposition date deposition_date	2004-03-16
Structure title title	Crystal structure of NS-134 in complex with bovine cathepsin B: a two headed epoxysuccinyl inhibitor extends along the whole active site cleft
Keywords keywords	cathepsin B, epoxysuccinyl-based inhibitors, inhibitor design, HYDROLASE, 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.

1sp4__assembly_1__model_1

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

Download this curve (.dat)

1sp4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1sp4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.18 Å
Rg (electron density)	17.15 Å
Total Rg	18.18 Å
Atom count	1967
Residues	253
Excluded volume	34303 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1sp4__assembly_1__model_1`	dimeric （2）	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 B
Molecular weight formula_weight	5300.9 kDa
EC 编号 ec_number	3.4.22.1
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	2143

LPESFDAREQWPNCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHSNG

Entity 2 Entity 2 polymer

Description description	Cathepsin B
Molecular weight formula_weight	22233.7 kDa
EC 编号 ec_number	3.4.22.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

RVNVEVSAEDMLTCCGGECGDGCNGGFPSGAWNFWTKKGLVSGGLYNSHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCNKTCEPGYSPSYKEDKHFGCSSYSVANNEKEIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVSGEIMGGHAIRILGWGVENGTPYWLVGNSWNTDWGDNGFFKILRGQDHCGIESEIVAGMPCT

Entity 3 Entity 3 non-polymer

Description description	;methyl N-[(2S)-4-{[(1S)-1-{[(2S)-2-carboxypyrrolidin-1-yl]carbonyl}-3-methylbutyl]amino}-2-hydroxy-4-oxobutanoyl]-L-leucylglycylglycinate ;
Molecular weight formula_weight	583.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1sp4.1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

CATH v4.4 (2 domains)

Domain ID domain_id	1sp4A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	1sp4B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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Unit-cell length a length_a	73.064 Å
Unit-cell length b length_b	73.064 Å
Unit-cell length c length_c	141.970 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1940
R_free r_free	—

Crystal structure of NS-134 in complex with bovine cathepsin B: a two headed epoxysuccinyl inhibitor extends along the whole active site cleft

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

Cathepsin B

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

1sp4__assembly_1__model_1

1sp4__assembly_1__model_1 | I(q)

1sp4__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of NS-134 in complex with bovine cathepsin B: a two headed epoxysuccinyl inhibitor extends along the whole active site cleft

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

Cathepsin B

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

1sp4__assembly_1__model_1

1sp4__assembly_1__model_1 | I(q)

1sp4__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)