2J0T

Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1

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	d2j0ta_	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	d2j0tb_	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)
C	d2j0tc_	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)
D	d2j0td_	All beta proteins	OB-fold	TIMP-like	Tissue inhibitor of metalloproteinases, TIMP	TIMP-1	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2j0te_	All beta proteins	OB-fold	TIMP-like	Tissue inhibitor of metalloproteinases, TIMP	TIMP-1	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2j0tf_	All beta proteins	OB-fold	TIMP-like	Tissue inhibitor of metalloproteinases, TIMP	TIMP-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)
B	SCOP2B Superfamily	Metalloproteases (zincins) catalytic domain	8039035	3001975	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metalloproteases (zincins) catalytic domain	8039035	3001975	SCOP2B (2022-06-29)
D	SCOP2 Family	Tissue inhibitor of metalloproteinases TIMP	8030576	4001872	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	TIMP-like	8042955	3000488	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	TIMP-like	8042955	3000488	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TIMP-like	8042955	3000488	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	Peptidase_M10	e2j0tA1	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	Peptidase_M10	e2j0tB1	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)
C	Peptidase_M10	e2j0tC1	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)
D	TIMP	e2j0tD1	A: beta barrels	X: OB-fold	H: TIMP-like (From Topology)	T: TIMP-like	F: TIMP	ECOD (1.6)
E	TIMP	e2j0tE1	A: beta barrels	X: OB-fold	H: TIMP-like (From Topology)	T: TIMP-like	F: TIMP	ECOD (1.6)
F	TIMP	e2j0tF1	A: beta barrels	X: OB-fold	H: TIMP-like (From Topology)	T: TIMP-like	F: TIMP	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)
B	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
C	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
D	2.40.50.120	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
E	2.40.50.120	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
F	2.40.50.120	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00413	Matrixin (Peptidase_M10)	Matrixin	The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.	Domain
D, E, F	PF00965	Tissue inhibitor of metalloproteinase (TIMP)	Tissue inhibitor of metalloproteinase	Members of this family are common in extracellular regions of vertebrate species	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	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
D, E, F	METALLOPROTEINASE INHIBITOR 1	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity enzyme binding protease binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity enzyme binding protease binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity metalloendopeptidase inhibitor activity endopeptidase inhibitor activity cytokine activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development response to organic substance response to stimulus response to hormone response to chemical developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development response to organic substance response to stimulus response to hormone response to chemical response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to oxygen-containing compound response to nitrogen compound regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death wound healing connective tissue replacement involved in inflammatory response wound healing wound healing involved in inflammatory response defense response response to stress inflammatory response to wounding tissue remodeling connective tissue replacement inflammatory response response to wounding response to cytokine regulation of molecular function regulation of catalytic activity negative regulation of molecular function negative regulation of catalytic activity cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of biological process positive regulation of cellular process negative regulation of hydrolase activity negative regulation of proteolysis regulation of primary metabolic process negative regulation of peptidase activity organic substance metabolic process regulation of proteolysis proteolysis protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process organonitrogen compound metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of peptidase activity primary metabolic process regulation of macromolecule metabolic process regulation of metallopeptidase activity regulation of hydrolase activity negative regulation of metallopeptidase activity metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of endopeptidase activity regulation of endopeptidase activity multi-multicellular organism process negative regulation of locomotion regulation of cell motility regulation of trophoblast cell migration regulation of reproductive process reproductive process ameboidal-type cell migration regulation of cell migration cell migration regulation of multicellular organismal process cell motility female pregnancy embryo implantation negative regulation of trophoblast cell migration locomotion negative regulation of cell migration trophoblast cell migration negative regulation of reproductive process regulation of locomotion negative regulation of cell motility negative regulation of multicellular organismal process multi-organism reproductive process negative regulation of membrane protein ectodomain proteolysis negative regulation of cellular catabolic process catabolic process macromolecule catabolic process negative regulation of cellular metabolic process negative regulation of protein catabolic process cellular catabolic process membrane protein proteolysis membrane protein ectodomain proteolysis organonitrogen compound catabolic process negative regulation of catabolic process regulation of membrane protein ectodomain proteolysis cellular metabolic process regulation of cellular metabolic process regulation of catabolic process protein catabolic process regulation of cellular catabolic process organic substance catabolic process regulation of protein catabolic process cellular response to stimulus regulation of integrin-mediated signaling pathway regulation of signaling integrin-mediated signaling pathway cell surface receptor signaling pathway signaling regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication signal transduction response to light 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	basement membrane cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle basement membrane cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen endoplasmic reticulum cytoplasm vesicle lumen intracellular vesicle cytoplasmic vesicle lumen secretory granule lumen cytoplasmic vesicle secretory granule secretory vesicle platelet alpha granule platelet alpha granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR018486	Hemopexin, conserved site	Conserved Site
A, B, C	IPR036375	Hemopexin-like domain superfamily	Homologous Superfamily
A, B, C	IPR021158	Peptidase M10A, cysteine switch, zinc binding site	Binding Site
A, B, C	IPR036365	PGBD-like superfamily	Homologous Superfamily
A, B, C	IPR001818	Peptidase M10, metallopeptidase	Domain
A, B, C	IPR021190	Peptidase M10A	Family
A, B, C	IPR002477	Peptidoglycan binding-like	Domain
A, B, C	IPR006026	Peptidase, metallopeptidase	Domain
A, B, C	IPR024079	Metallopeptidase, catalytic domain superfamily	Homologous Superfamily
A, B, C	IPR018487	Hemopexin-like repeats	Repeat
A, B, C	IPR000585	Hemopexin-like domain	Domain
A, B, C	IPR033739	Peptidase M10A, catalytic domain	Domain
D, E, F	IPR001820	Protease inhibitor I35 (TIMP)	Family
D, E, F	IPR027465	Proteinase inhibitor I35b (TIMP), C-terminal	Homologous Superfamily
D, E, F	IPR001134	Netrin domain	Domain
D, E, F	IPR008993	Tissue inhibitor of metalloproteinases-like, OB-fold	Homologous Superfamily
D, E, F	IPR030490	Tissue inhibitor of metalloproteinase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	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
D, E, F	Pharos: P01033	aortic valve insufficiency Wilson disease oral submucous fibrosis IgA glomerulonephritis heart disease hypertensive disorder type 2 diabetes mellitus Inflammation vascular disease adult acute respiratory distress syndrome cholangitis extrahepatic cholestasis pulmonary fibrosis heart valve disease alcoholic liver cirrhosis aortic valve insufficiency Wilson disease oral submucous fibrosis IgA glomerulonephritis heart disease hypertensive disorder type 2 diabetes mellitus Inflammation vascular disease adult acute respiratory distress syndrome cholangitis extrahepatic cholestasis pulmonary fibrosis heart valve disease alcoholic liver cirrhosis autoimmune disease calcinosis varicose disease osteosarcoma esophageal adenocarcinoma pilocytic astrocytoma gastric carcinoma subependymal giant cell astrocytoma juvenile dermatomyositis liver disease Becker muscular dystrophy malignant colon neoplasm malignant mesothelioma medulloblastoma ductal breast carcinoma in situ ovarian cancer glioblastoma tuberculosis idiopathic interstitial pneumonia ulcerative colitis interstitial cystitis limb-girdle muscular dystrophy lung adenocarcinoma malignant ependymoma congestive heart failure malignant pancreatic neoplasm diabetes mellitus Emery-Dreifuss muscular dystrophy pancreatic ductal adenocarcinoma invasive ductal breast carcinoma Barrett esophagus lung cancer cancer malignant glioma Crohn disease maturity-onset diabetes of the young myopathy Duchenne muscular dystrophy

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.