1SU3

X-ray structure of human proMMP-1: New insights into collagenase action

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1su3a1	All alpha proteins	PGBD-like	PGBD-like	MMP N-terminal domain	Fibroblast collagenase (MMP-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1su3a2	All beta proteins	4-bladed beta-propeller	Hemopexin-like domain	Hemopexin-like domain	Collagenase (MMP1), C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1su3a3	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Fibroblast collagenase (MMP-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1su3b1	All alpha proteins	PGBD-like	PGBD-like	MMP N-terminal domain	Fibroblast collagenase (MMP-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1su3b2	All beta proteins	4-bladed beta-propeller	Hemopexin-like domain	Hemopexin-like domain	Collagenase (MMP1), C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1su3b3	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Fibroblast collagenase (MMP-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metalloproteases (zincins) catalytic domain	8039035	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PGBD-like	8042355	3001357	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Hemopexin-like domain	8042356	3001566	SCOP2B (2022-06-29)
B	SCOP2 Family	MMP N-terminal domain	8029976	4002891	SCOP2 (2022-06-29)
B	SCOP2 Family	Hemopexin-like domain	8029977	4002660	SCOP2 (2022-06-29)
B	SCOP2 Family	Matrix metalloproteases catalytic domain	8026656	4001637	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PGBD-like	8042355	3001357	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Hemopexin-like domain	8042356	3001566	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Metalloproteases (zincins) catalytic domain	8039035	3001975	SCOP2 (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	Hemopexin	e1su3A1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 4-bladed	F: Hemopexin	ECOD (1.6)
A	PG_binding_1	e1su3A2	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: PG_binding_1	ECOD (1.6)
A	Peptidase_M10	e1su3A3	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M10	ECOD (1.6)
B	Hemopexin	e1su3B1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 4-bladed	F: Hemopexin	ECOD (1.6)
B	PG_binding_1	e1su3B2	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: PG_binding_1	ECOD (1.6)
B	Peptidase_M10	e1su3B3	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M10	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
A	2.110.10.10	Mainly Beta	4 Propeller	Hemopexin	Hemopexin-like domain	CATH (4.3.0)
B	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
B	2.110.10.10	Mainly Beta	4 Propeller	Hemopexin	Hemopexin-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00413	Matrixin (Peptidase_M10)	Matrixin	The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.	Domain
A, B	PF01471	Putative peptidoglycan binding domain (PG_binding_1)	Putative peptidoglycan binding domain	This domain is composed of three alpha helices [1]. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [2]. This domain may have a general peptidoglycan binding function. This family is ...	This domain is composed of three alpha helices [1]. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [2]. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins [3]. The domain is found to bind peptidoglycan experimentally [4].	Domain
A, B	PF00045	Hemopexin (Hemopexin)	Hemopexin	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Interstitial collagenase	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity metalloendopeptidase activity metallopeptidase activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity cation binding transition metal ion binding zinc ion binding ion binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity metalloendopeptidase activity metallopeptidase activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	collagen catabolic process catabolic process metabolic process collagen metabolic process regulation of biological process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis biological regulation positive regulation of biological process regulation of cellular component biogenesis cellular component organization collagen catabolic process catabolic process metabolic process collagen metabolic process regulation of biological process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis biological regulation positive regulation of biological process regulation of cellular component biogenesis cellular component organization cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis positive regulation of cellular process extracellular matrix organization extracellular structure organization external encapsulating structure organization cellular component disassembly extracellular matrix disassembly organic substance metabolic process organonitrogen compound metabolic process primary metabolic process protein metabolic process macromolecule metabolic process response to light stimulus cellular response to stimulus response to stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to UV-A cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV response to UV-A proteolysis	cell periphery extracellular matrix external encapsulating structure cellular anatomical entity extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018486	Hemopexin, conserved site	Conserved Site
A, B	IPR036375	Hemopexin-like domain superfamily	Homologous Superfamily
A, B	IPR021158	Peptidase M10A, cysteine switch, zinc binding site	Binding Site
A, B	IPR036365	PGBD-like superfamily	Homologous Superfamily
A, B	IPR001818	Peptidase M10, metallopeptidase	Domain
A, B	IPR021190	Peptidase M10A	Family
A, B	IPR002477	Peptidoglycan binding-like	Domain
A, B	IPR006026	Peptidase, metallopeptidase	Domain
A, B	IPR024079	Metallopeptidase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR018487	Hemopexin-like repeats	Repeat
A, B	IPR000585	Hemopexin-like domain	Domain
A, B	IPR033739	Peptidase M10A, catalytic domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P03956	oral submucous fibrosis epidermolysis bullosa dystrophica non-small cell lung carcinoma breast carcinoma non-alcoholic fatty liver disease ocular hypertension Liver Cirrhosis, Experimental atherosclerosis breast cancer colorectal cancer ovarian cancer digestive system disease psoriasis epilepsy ulcerative colitis oral submucous fibrosis epidermolysis bullosa dystrophica non-small cell lung carcinoma breast carcinoma non-alcoholic fatty liver disease ocular hypertension Liver Cirrhosis, Experimental atherosclerosis breast cancer colorectal cancer ovarian cancer digestive system disease psoriasis epilepsy ulcerative colitis invasive ductal breast carcinoma lung benign neoplasm malignant mesothelioma Barrett esophagus malignant pancreatic neoplasm cancer nasopharyngeal carcinoma chronic obstructive pulmonary disease colorectal carcinoma cutaneous lupus erythematosus periodontitis ductal breast carcinoma in situ recessive dystrophic epidermolysis bullosa esophageal adenocarcinoma vascular disease IgA glomerulonephritis arteriosclerosis disorder lung cancer cystic fibrosis peripheral arterial disease epidermolysis bullosa interstitial cystitis lung adenocarcinoma arthritic joint disease atopic eczema COPD, severe early onset

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.