SAXSdb — 2r9f

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

Calpain-1 catalytic subunit

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 CHLORIDE ION × 3 ;benzyl [(1S)-1-{[(1S,2S)-1-ethyl-2-hydroxy-3-{[3-(4-methylpiperazin-1-yl)propyl]amino}-3-oxopropyl]carbamoyl}-3-methylbutyl]carbamate ; × 1 GLYCEROL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAN1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–331； UniProt 27–356

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	2r9f
Deposition date deposition_date	2007-09-12
Structure title title	Calpain 1 proteolytic core inactivated by ZLAK-3002, an alpha-ketoamide
Keywords keywords	PROTEASE, PEPTIDASE, INHIBITOR, ALPHA-KETOAMIDE, Hydrolase, Membrane, Thiol protease; HYDROLASE
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.

2r9f__assembly_1__model_1

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

Download this curve (.dat)

2r9f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r9f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.89 Å
Rg (electron density)	20.83 Å
Total Rg	21.73 Å
Atom count	2648
Residues	322
Excluded volume	47108 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r9f__assembly_1__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	Calpain-1 catalytic subunit
Molecular weight formula_weight	38804.6 kDa
EC 编号 ec_number	3.4.22.52
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	2985

MGLGRHENAIKYLGQDYENLRARCLQNGVLFQDDAFPPVSHSLGFKELGPNSSKTYGIKWKRPTELLSNPQFIVDGATRTDICQGALGDCWLLAAIASLTLNETILHRVVPYGQSFQEGYAGIFHFQLWQFGEWVDVVVDDLLPTKDGKLVFVHSAQGNEFWSALLEKAYAKVNGSYEALSGGCTSEAFEDFTGGVTEWYDLQKAPSDLYQIILKALERGSLLGCSINISDIRDLEAITFKNLVRGHAYSVTDAKQVTYQGQRVNLIRMRNPWGEVEWKGPWSDNSYEWNKVDPYEREQLRVKMEDGEFWMSFRDFIREFTKLEICNLTPDLEHHHHHH

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	;benzyl [(1S)-1-{[(1S,2S)-1-ethyl-2-hydroxy-3-{[3-(4-methylpiperazin-1-yl)propyl]amino}-3-oxopropyl]carbamoyl}-3-methylbutyl]carbamate ;
Molecular weight formula_weight	519.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	268

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2r9fa_
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.3.1.3 — Calpain large subunit, catalytic domain (domain II)

CATH v4.4 (1 domains)

Domain ID domain_id	2r9fA02
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	40.569 Å
Unit-cell length b length_b	70.568 Å
Unit-cell length c length_c	110.406 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	4

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	35.290 Å
R factor r_factor	0.1906
R_work r_work	0.1889
R_free r_free	0.2217

Calpain 1 proteolytic core inactivated by ZLAK-3002, an alpha-ketoamide

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

Calpain-1 catalytic subunit

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

2r9f__assembly_1__model_1

2r9f__assembly_1__model_1 | I(q)

2r9f__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Calpain 1 proteolytic core inactivated by ZLAK-3002, an alpha-ketoamide

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

Calpain-1 catalytic subunit

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

2r9f__assembly_1__model_1

2r9f__assembly_1__model_1 | I(q)

2r9f__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)