4DPE | pdb_00004dpe

Structure of MMP3 complexed with a platinum-based inhibitor.

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	d4dpea_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Stromelysin-1 (MMP-3)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4dpeb_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Stromelysin-1 (MMP-3)	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	8035528	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8035528	3001975	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		e4dpeA1	A: Alpha-beta plaits	X: Family B DNA polymerase insertion domain	H: Family B DNA polymerase insertion domain	T: Oxidored_q6	F:	ECOD (20:10:01)
B		e4dpeB1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)

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)

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Stromelysin-1	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity metalloendopeptidase 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 metallopeptidase activity hydrolase activity catalytic activity metalloendopeptidase 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 cellular process collagen metabolic process regulation of biological process regulation of cellular process positive regulation of cellular component organization 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 collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process regulation of biological process regulation of cellular process positive regulation of cellular component organization 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 component organization or biogenesis positive regulation of cellular process extracellular matrix organization extracellular structure organization external encapsulating structure organization regulation of defense response response to stimulus regulation of response to external stimulus defense response regulation of inflammatory response response to external stimulus regulation of response to stimulus response to stress regulation of response to stress regulation of neuroinflammatory response inflammatory response neuroinflammatory response biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process cellular response to stimulus response to lipid cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to molecule of bacterial origin cellular component disassembly extracellular matrix disassembly regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion response to nitrogen compound response to amyloid-beta negative regulation of metabolic process reactive oxygen species metabolic process negative regulation of biological process negative regulation of reactive oxygen species metabolic process negative regulation of cellular process regulation of metabolic process regulation of reactive oxygen species metabolic process cellular response to oxidative stress cellular response to chemical stress response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress cellular response to stress cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B 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 proteolysis cellular response to nitrogen compound cellular response to nitric oxide response to nitric oxide cellular response to reactive nitrogen species	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol cell periphery extracellular matrix external encapsulating structure extracellular region extracellular space membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol cell periphery extracellular matrix external encapsulating structure extracellular region extracellular space nucleus

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: P08254	protoplasmic astrocytoma subependymal giant cell astrocytoma gemistocytic astrocytoma idiopathic pulmonary fibrosis astrocytic tumor coronary artery disease peripheral neuropathy coronary restenosis anaplastic astrocytoma breast cancer Neoplasm Invasiveness childhood cerebral astrocytoma pilocytic astrocytoma fibrillary astrocytoma juvenile pilocytic astrocytoma protoplasmic astrocytoma subependymal giant cell astrocytoma gemistocytic astrocytoma idiopathic pulmonary fibrosis astrocytic tumor coronary artery disease peripheral neuropathy coronary restenosis anaplastic astrocytoma breast cancer Neoplasm Invasiveness childhood cerebral astrocytoma pilocytic astrocytoma fibrillary astrocytoma juvenile pilocytic astrocytoma breast carcinoma peripheral nervous system disease coronary heart disease, susceptibility to, 6 diffuse astrocytoma ulcerative colitis intracerebral hemorrhage malignant colon neoplasm bipolar disorder breast fibroadenoma nasopharyngeal carcinoma periodontitis psoriasis ductal breast carcinoma in situ synovitis interstitial cystitis astrocytoma (excluding glioblastoma) cancer peripheral arterial disease cystic fibrosis schizophrenia arthritic joint disease intervertebral disc degenerative disorder autoimmune disease cerebral astrocytoma non-small cell lung carcinoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.