3KRY | pdb_00003kry

Crystal structure of MMP-13 in complex with SC-78080

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)
D	d3kryd_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Collagenase-3 (MMP-13)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3kryc_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Collagenase-3 (MMP-13)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3kryb_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Collagenase-3 (MMP-13)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3krya_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Matrix metalloproteases, catalytic domain	Collagenase-3 (MMP-13)	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)
D	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8033902	3001975	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8033902	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8033902	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8033902	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)
D		e3kryD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (v294.1)
C		e3kryC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (v294.1)
B		e3kryB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (v294.1)
A		e3kryA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
B	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
A	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, C, D	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, C, D	Collagenase 3	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity serine hydrolase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity collagen binding protein-containing complex binding transition metal ion binding zinc ion binding	multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process growth animal organ development tissue development anatomical structure morphogenesis bone growth skeletal system morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis cartilage development collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process ossification bone mineralization biomineral tissue development cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization endochondral ossification replacement ossification cellular component disassembly extracellular matrix disassembly response to stimulus response to chemical response to oxygen-containing compound response to nitrogen compound response to amyloid-beta proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	extracellular matrix cellular anatomical structure external encapsulating structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P45452	spondyloepimetaphyseal dysplasia, Missouri type metaphyseal chondrodysplasia, Spahr type prostate cancer Craniofacial Abnormalities metaphyseal anadysplasia breast cancer cutaneous lupus erythematosus intervertebral disc degenerative disorder lung adenocarcinoma osteoarthritis spondyloepiphyseal dysplasia chronic obstructive pulmonary disease head and neck cancer invasive ductal breast carcinoma malignant colon neoplasm spondyloepimetaphyseal dysplasia, Missouri type metaphyseal chondrodysplasia, Spahr type prostate cancer Craniofacial Abnormalities metaphyseal anadysplasia breast cancer cutaneous lupus erythematosus intervertebral disc degenerative disorder lung adenocarcinoma osteoarthritis spondyloepiphyseal dysplasia chronic obstructive pulmonary disease head and neck cancer invasive ductal breast carcinoma malignant colon neoplasm osteogenesis imperfecta synovitis intellectual disability non-small cell lung carcinoma periodontitis

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.