6BKJ

Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cysteine proteinases	8062474	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8062474	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8062474	3001808	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cysteine proteinases	8062474	3001808	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00648	e6bkjA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00648	ECOD (1.6)
B	PF00648	e6bkjB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00648	ECOD (1.6)
C	PF00648	e6bkjC1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00648	ECOD (1.6)
D	PF00648	e6bkjD1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00648	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
D	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00648	Calpain family cysteine protease (Peptidase_C2)	Calpain family cysteine protease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Calpain-3	cytoskeletal protein binding titin binding protein binding binding structural molecule activity structural constituent of muscle cysteine-type peptidase activity peptidase activity calcium-dependent cysteine-type endopeptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity cytoskeletal protein binding titin binding protein binding binding structural molecule activity structural constituent of muscle cysteine-type peptidase activity peptidase activity calcium-dependent cysteine-type endopeptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity enzyme regulator activity molecular function regulator activity ligase regulator activity molecular adaptor activity cation binding ion binding alkali metal ion binding sodium ion binding metal ion binding small molecule binding identical protein binding calcium ion binding	response to stimulus response to activity response to muscle activity protein destabilization regulation of protein stability biological regulation regulation of biological quality response to metal ion response to chemical response to calcium ion response to inorganic substance cellular process apoptotic process cell death response to stimulus response to activity response to muscle activity protein destabilization regulation of protein stability biological regulation regulation of biological quality response to metal ion response to chemical response to calcium ion response to inorganic substance cellular process apoptotic process cell death programmed cell death organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process developmental process muscle structure development animal organ development anatomical structure development muscle organ development cellular response to stimulus cellular response to inorganic substance cellular response to metal ion cellular response to chemical stimulus cellular response to calcium ion regulation of biological process positive regulation of protein metabolic process regulation of protein metabolic process positive regulation of biological process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of proteolysis proteolysis positive regulation of proteolysis positive regulation of macromolecule metabolic process regulation of metabolic process positive regulation of DNA-binding transcription factor activity regulation of cellular process cellular biosynthetic process positive regulation of NF-kappaB transcription factor activity RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of molecular function organic cyclic compound metabolic process regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription protein localization localization cellular localization cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane positive regulation of skeletal muscle tissue regeneration tissue regeneration multicellular organismal process regulation of growth skeletal muscle tissue regeneration skeletal muscle satellite cell activation regulation of response to external stimulus regulation of developmental process developmental growth regulation of cell activation regeneration positive regulation of satellite cell activation involved in skeletal muscle regeneration positive regulation of developmental process multicellular organism development positive regulation of cell activation satellite cell activation involved in skeletal muscle regeneration regulation of multicellular organismal process positive regulation of developmental growth positive regulation of cellular process regulation of multicellular organismal development regulation of developmental growth growth cell activation response to external stimulus positive regulation of growth regulation of satellite cell activation involved in skeletal muscle regeneration regulation of response to stimulus regulation of skeletal muscle tissue regeneration positive regulation of multicellular organismal process response to osmotic stress cellular response to salt stress cellular response to chemical stress cellular response to osmotic stress response to salt stress cellular response to environmental stimulus cellular response to stress response to stress response to abiotic stimulus cellular response to abiotic stimulus G1 to G0 transition involved in cell differentiation cellular developmental process cell differentiation cell cycle G1 to G0 transition cell cycle process regulation of cell differentiation regulation of myoblast differentiation myoblast differentiation cellular homeostasis homeostatic process muscle cell cellular homeostasis negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process self proteolysis cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process calcium-dependent self proteolysis regulation of catalytic activity positive regulation of macromolecule biosynthetic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulation of calcium ion transport regulation of localization positive regulation of cation transmembrane transport positive regulation of calcium ion transport intracellular calcium ion homeostasis calcium ion transport positive regulation of monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation homeostasis monoatomic cation transport intracellular monoatomic ion homeostasis regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport chemical homeostasis inorganic ion homeostasis transport monoatomic ion transmembrane transport calcium ion homeostasis regulation of monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion metal ion transport maintenance of location in cell regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport intracellular monoatomic cation homeostasis monoatomic ion homeostasis positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport intracellular chemical homeostasis positive regulation of release of sequestered calcium ion into cytosol regulation of metal ion transport regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol regulation of transport sequestering of calcium ion positive regulation of transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport cellular component assembly involved in morphogenesis non-membrane-bounded organelle assembly cell development muscle cell differentiation striated muscle cell development cellular anatomical entity morphogenesis muscle cell development actin filament-based process actomyosin structure organization actin cytoskeleton organization organelle assembly anatomical structure morphogenesis myofibril assembly organelle organization anatomical structure formation involved in morphogenesis striated muscle cell differentiation supramolecular fiber organization cytoskeleton organization negative regulation of post-translational protein modification regulation of protein sumoylation regulation of protein modification process peptidyl-lysine modification peptidyl-amino acid modification negative regulation of protein modification process protein modification process regulation of protein modification by small protein conjugation or removal negative regulation of protein sumoylation negative regulation of protein metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification protein sumoylation macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal sarcomere organization regulation of signaling signaling regulation of signal transduction intracellular signal transduction canonical NF-kappaB signal transduction cell communication regulation of intracellular signal transduction intracellular signaling cassette regulation of cell communication regulation of canonical NF-kappaB signal transduction signal transduction	cell periphery sarcolemma plasma membrane membrane T-tubule cellular anatomical entity intracellular anatomical structure Z disc sarcomere intracellular organelle I band organelle intracellular non-membrane-bounded organelle contractile muscle fiber cell periphery sarcolemma plasma membrane membrane T-tubule cellular anatomical entity intracellular anatomical structure Z disc sarcomere intracellular organelle I band organelle intracellular non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex non-membrane-bounded organelle cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen protein-containing complex
E [auth F], F [auth G], G [auth H], H [auth I]	Leupeptin	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR022684	Peptidase C2, calpain family	Family
A, B, C, D	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D	IPR002048	EF-hand domain	Domain
A, B, C, D	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
A, B, C, D	IPR033883	Calpain subdomain III	Domain
A, B, C, D	IPR036213	Calpain large subunit, domain III superfamily	Homologous Superfamily
A, B, C, D	IPR022682	Peptidase C2, calpain, large subunit, domain III	Domain
A, B, C, D	IPR000169	Cysteine peptidase, cysteine active site	Active Site
A, B, C, D	IPR011992	EF-hand domain pair	Homologous Superfamily
A, B, C, D	IPR001300	Peptidase C2, calpain, catalytic domain	Domain
A, B, C, D	IPR022683	Peptidase C2, calpain, domain III	Domain
A, B, C, D	IPR029531	Calpain-3, penta-EF-hand	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P20807	limb-girdle muscular dystrophy autosomal recessive limb-girdle muscular dystrophy type 2A myopathy arthrogryposis muscular disease Limb-girdle muscular dystrophy type 2A muscular dystrophy muscle tissue disease

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth F], F [auth G], G [auth H], H [auth I]	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
E [auth F], F [auth G], G [auth H], H [auth I]	AR7	Parent Component: ARG RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.