3DNG

Crystal structure of the complex between MMP-8 and a non-zinc chelating 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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3dnga_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Neutrophil collagenase (MMP-8)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3dngb_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Neutrophil collagenase (MMP-8)	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	8033729	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metalloproteases (zincins) catalytic domain	8033729	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	Peptidase_M10	e3dngA1	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	e3dngB1	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)
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	Neutrophil 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 protein binding binding cytokine binding tumor necrosis factor 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 protein binding binding cytokine binding tumor necrosis factor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	collagen catabolic process catabolic process metabolic process collagen metabolic process cellular response to stimulus positive regulation of cell communication response to organic substance regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process response to cytokine regulation of signal transduction collagen catabolic process catabolic process metabolic process collagen metabolic process cellular response to stimulus positive regulation of cell communication response to organic substance regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus cellular response to organic substance signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway biological regulation regulation of response to cytokine stimulus cellular response to chemical stimulus regulation of response to stimulus response to chemical regulation of cell communication cellular process response to tumor necrosis factor positive regulation of cytokine-mediated signaling pathway positive regulation of signaling developmental process multicellular organismal process formation of primary germ layer cellular developmental process embryonic morphogenesis tissue development embryo development gastrulation anatomical structure morphogenesis multicellular organism development endoderm development cell differentiation anatomical structure development anatomical structure formation involved in morphogenesis endoderm formation endodermal cell differentiation cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus 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 cellular component disassembly extracellular matrix disassembly regulation of macrophage activation regulation of defense response positive regulation of macrophage activation regulation of response to external stimulus regulation of leukocyte activation positive regulation of microglial cell activation regulation of cell activation positive regulation of neuroinflammatory response myeloid leukocyte activation leukocyte activation macrophage activation positive regulation of cell activation positive regulation of response to external stimulus positive regulation of inflammatory response response to stress regulation of response to stress leukocyte activation involved in inflammatory response regulation of neuroinflammatory response positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process positive regulation of immune system process defense response cell activation regulation of inflammatory response immune system process positive regulation of defense response positive regulation of multicellular organismal process microglial cell activation inflammatory response glial cell activation regulation of microglial cell activation neuroinflammatory response regulation of tumor necrosis factor production cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of tumor necrosis factor superfamily cytokine production organic substance metabolic process positive regulation of biosynthetic process cytokine production organic substance biosynthetic process regulation of cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process tumor necrosis factor superfamily cytokine production regulation of cellular metabolic process positive regulation of tumor necrosis factor production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of cellular biosynthetic process regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process positive regulation of cellular biosynthetic process organonitrogen compound metabolic process proteolysis nitrogen compound metabolic process primary metabolic process protein metabolic process	cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity membrane-bounded organelle intracellular anatomical structure tertiary granule lumen membrane-enclosed lumen intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen tertiary granule cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity membrane-bounded organelle intracellular anatomical structure tertiary granule lumen membrane-enclosed lumen intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen tertiary granule intracellular organelle organelle lumen cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle extracellular region vesicle lumen cytoplasmic vesicle lumen secretory granule lumen specific granule lumen specific granule 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: P22894	melanoma contact dermatitis Liver Cirrhosis, Experimental epilepsy preterm premature rupture of the membranes gingivitis major depressive disorder osteosarcoma cutaneous melanoma injury lung disease MALT lymphoma periodontitis

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.