4JIJ

Crystal structure of an inactive mutant of MMP-9 catalytic domain in complex with a fluorogenic synthetic peptidic substrate

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)
B [auth A]	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8043702	3001975	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8043702	3001975	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8043702	3001975	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8043702	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)
B [auth A]	Peptidase_M10	e4jijA1	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 [auth B]	Peptidase_M10	e4jijB1	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)
B [auth A]	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
D [auth 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
B [auth A], D [auth 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 [auth P], C [auth Q]	fluorogenic peptidic substrate (8MC)PLG(PHI)(DNW)AR(NH2)	-	-	-
B [auth A], D [auth B]	Matrix metalloproteinase-9	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein binding binding metalloendopeptidase activity collagen binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein binding binding metalloendopeptidase activity collagen binding protein-containing complex binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA binding cellular response to stimulus positive regulation of organelle organization regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization response to stimulus signaling regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA binding cellular response to stimulus positive regulation of organelle organization regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization response to stimulus signaling apoptotic mitochondrial changes positive regulation of biological process regulation of release of cytochrome c from mitochondria cell communication cellular component organization positive regulation of release of cytochrome c from mitochondria cellular component organization or biogenesis signal transduction positive regulation of cellular process mitochondrion organization regulation of biological process cell death regulation of organelle organization apoptotic signaling pathway release of cytochrome c from mitochondria organelle organization regulation of mitochondrion organization cellular process apoptotic process programmed cell death developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development system development cell surface receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway extracellular matrix organization extracellular structure organization external encapsulating structure organization regulation of defense response 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 positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of response to stimulus positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway regulation of signaling ERBB signaling pathway regulation of cell communication positive regulation of signaling cell migration cell motility regulation of protein binding regulation of receptor binding positive regulation of protein binding positive regulation of receptor binding positive regulation of locomotion regulation of cell motility regulation of keratinocyte migration positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration regulation of multicellular organismal process epithelial cell migration regulation of epithelial cell migration locomotion epithelium migration regulation of locomotion positive regulation of keratinocyte migration keratinocyte migration cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to cadmium ion response to cadmium ion collagen catabolic process catabolic process metabolic process collagen metabolic process negative regulation of programmed cell death negative regulation of biological process negative regulation of apoptotic process negative regulation of cellular process formation of primary germ layer cellular developmental process embryonic morphogenesis tissue development embryo development gastrulation anatomical structure morphogenesis endoderm development cell differentiation anatomical structure formation involved in morphogenesis endoderm formation endodermal cell differentiation regulation of developmental process negative regulation of epithelial cell differentiation involved in kidney development regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation renal system development regulation of epithelial cell differentiation involved in kidney development negative regulation of cell differentiation epithelial cell differentiation involved in kidney development epithelium development regulation of multicellular organismal development negative regulation of epithelial cell differentiation negative regulation of developmental process animal organ development cell differentiation involved in kidney development kidney development regulation of vascular associated smooth muscle cell proliferation cell population proliferation positive regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation biological process involved in interspecies interaction between organisms response to lipid response to other organism 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 response to biotic stimulus cellular response to biotic stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin regulation of localization negative regulation of ion transmembrane transporter activity negative regulation of cation channel activity transport monoatomic ion transmembrane transport negative regulation of monoatomic ion transport regulation of transmembrane transporter activity negative regulation of transport regulation of monoatomic ion transmembrane transport negative regulation of transmembrane transport regulation of transporter activity monoatomic cation transmembrane transport localization negative regulation of monoatomic ion transmembrane transport negative regulation of cation transmembrane transport monoatomic ion transport monoatomic cation transport regulation of monoatomic ion transmembrane transporter activity regulation of transport regulation of monoatomic ion transport negative regulation of transporter activity negative regulation of molecular function establishment of localization regulation of cation channel activity transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport cellular component disassembly extracellular matrix disassembly negative regulation of signaling negative regulation of intracellular signal transduction regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of intrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway multi-multicellular organism process reproductive process female pregnancy embryo implantation multi-organism reproductive process response to nitrogen compound response to amyloid-beta 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 myeloid leukocyte differentiation hemopoiesis macrophage differentiation cell development mononuclear cell differentiation myeloid cell differentiation leukocyte differentiation positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process negative regulation of proteolysis regulation of catalytic activity negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway negative regulation of catalytic activity negative regulation of peptidase activity regulation of proteolysis proteolysis negative regulation of cysteine-type endopeptidase activity involved in apoptotic process negative regulation of protein metabolic process regulation of cysteine-type endopeptidase activity negative regulation of metabolic process regulation of peptidase activity regulation of hydrolase activity negative regulation of cysteine-type endopeptidase activity regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway negative regulation of hydrolase activity negative regulation of endopeptidase activity regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of endopeptidase activity negative regulation of macromolecule metabolic process 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	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix intracellular anatomical structure membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle cytoplasm tertiary granule lumen tertiary granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], D [auth B]	IPR021158	Peptidase M10A, cysteine switch, zinc binding site	Binding Site
B [auth A], D [auth B]	IPR000562	Fibronectin type II domain	Domain
B [auth A], D [auth B]	IPR021190	Peptidase M10A	Family
B [auth A], D [auth B]	IPR006026	Peptidase, metallopeptidase	Domain
B [auth A], D [auth B]	IPR033739	Peptidase M10A, catalytic domain	Domain
B [auth A], D [auth B]	IPR018486	Hemopexin, conserved site	Conserved Site
B [auth A], D [auth B]	IPR036375	Hemopexin-like domain superfamily	Homologous Superfamily
B [auth A], D [auth B]	IPR036943	Fibronectin type II domain superfamily	Homologous Superfamily
B [auth A], D [auth B]	IPR036365	PGBD-like superfamily	Homologous Superfamily
B [auth A], D [auth B]	IPR001818	Peptidase M10, metallopeptidase	Domain
B [auth A], D [auth B]	IPR013806	Kringle-like fold	Homologous Superfamily
B [auth A], D [auth B]	IPR024079	Metallopeptidase, catalytic domain superfamily	Homologous Superfamily
B [auth A], D [auth B]	IPR018487	Hemopexin-like repeats	Repeat
B [auth A], D [auth B]	IPR000585	Hemopexin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A], D [auth B]	Pharos: P14780	abdominal aortic aneurysm metaphyseal anadysplasia 2 ulcerative colitis glioblastoma malignant colon neoplasm obesity disorder breast carcinoma thoracic aortic aneurysm periodontitis liver disease oral submucous fibrosis Marfan syndrome aortic aneurysm non-small cell lung carcinoma brain edema abdominal aortic aneurysm metaphyseal anadysplasia 2 ulcerative colitis glioblastoma malignant colon neoplasm obesity disorder breast carcinoma thoracic aortic aneurysm periodontitis liver disease oral submucous fibrosis Marfan syndrome aortic aneurysm non-small cell lung carcinoma brain edema squamous cell carcinoma hypertensive disorder Neointima brain ischemia subependymal giant cell astrocytoma diabetic polyneuropathy prostate cancer middle cerebral artery infarction aortic disease protoplasmic astrocytoma juvenile pilocytic astrocytoma asthma pulmonary fibrosis childhood cerebral astrocytoma morphine dependence retinal disease chronic obstructive pulmonary disease giant cell glioblastoma lupus nephritis skin neoplasm hyperplasia substance withdrawal syndrome acute coronary syndrome pilocytic astrocytoma astrocytic tumor gastric ulcer myocardial infarction bipolar disorder skin cancer diabetic autonomic neuropathy malignant pancreatic neoplasm diabetic neuropathy breast cancer calcinosis metaphyseal anadysplasia anaplastic astrocytoma extrahepatic cholestasis pulmonary emphysema lead poisoning fibrillary astrocytoma gemistocytic astrocytoma autoimmune disease lung disease cutaneous lupus erythematosus heart disease bone cancer skin disease Hodgkins lymphoma ovarian disease idiopathic interstitial pneumonia MALT lymphoma pancreatic intraductal papillary-mucinous neoplasm interstitial cystitis cancer drug-induced liver injury endogenous depression eye disease atypical teratoid rhabdoid tumor lung adenocarcinoma coronary artery disease cystic fibrosis benign colon neoplasm Sjogren syndrome hematologic disease malignant ependymoma stomach disease IgA glomerulonephritis diffuse astrocytoma pancreatic neoplasm inflammatory bowel disease breast disease intervertebral disc degenerative disorder celiac disease ductal breast carcinoma in situ prostate disease invasive ductal breast carcinoma cerebral astrocytoma vertebral column disease esophageal adenocarcinoma psoriasis kidney disease mucocutaneous lymph node syndrome atherosclerosis colonic disease autism spectrum disorder lung cancer Crohn disease head and neck cancer hepatocellular carcinoma malignant mesothelioma osteogenesis imperfecta brain injury pancreatic ductal adenocarcinoma inborn carbohydrate metabolic disorder mandibuloacral dysplasia with type A lipodystrophy diffuse large B-cell lymphoma age-related macular degeneration tuberculosis intracerebral hemorrhage ischemia reperfusion injury wet macular degeneration arthritic joint disease cerebrovascular disorder astrocytoma (excluding glioblastoma) multiple organ dysfunction syndrome attention deficit hyperactivity disorder, inattentive type schizophrenia lumbar disc degenerative disorder colonic neoplasm

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth P], C [auth Q]	8MC
A [auth P], C [auth Q]	DNW	Parent Component: ALA
A [auth P], C [auth Q]	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109
A [auth P], C [auth Q]	PHI	Parent Component: PHE RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100

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.