4NIY | pdb_00004niy

Crystal structure of trypsiligase (K60E/N143H/Y151H/D189K trypsin) complexed to YRH-ecotin (M84Y/M85R/A86H ecotin)

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4niya_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d4niyb_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C	d4niyc_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D	d4niyd_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
E	d4niye_	All beta proteins	Ecotin, trypsin inhibitor	Ecotin, trypsin inhibitor	Ecotin, trypsin inhibitor	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d4niyf_	All beta proteins	Ecotin, trypsin inhibitor	Ecotin, trypsin inhibitor	Ecotin, trypsin inhibitor	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G	d4niyg_	All beta proteins	Ecotin, trypsin inhibitor	Ecotin, trypsin inhibitor	Ecotin, trypsin inhibitor	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
H	d4niyh_	All beta proteins	Ecotin, trypsin inhibitor	Ecotin, trypsin inhibitor	Ecotin, trypsin inhibitor	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8037496	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8037496	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8037496	3000114	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8037496	3000114	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ecotin, trypsin inhibitor	8041127	3001256	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ecotin, trypsin inhibitor	8041127	3001256	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ecotin, trypsin inhibitor	8041127	3001256	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ecotin, trypsin inhibitor	8041127	3001256	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	Trypsin_1	e4niyA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
B	Trypsin_1	e4niyB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
C	Trypsin_1	e4niyC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
D	Trypsin_1	e4niyD2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
E	Ecotin	e4niyE1	A: beta sandwiches	X: Ecotin, trypsin inhibitor (From Topology)	H: Ecotin, trypsin inhibitor (From Topology)	T: Ecotin, trypsin inhibitor	F: Ecotin	ECOD (1.6)
F	Ecotin	e4niyF1	A: beta sandwiches	X: Ecotin, trypsin inhibitor (From Topology)	H: Ecotin, trypsin inhibitor (From Topology)	T: Ecotin, trypsin inhibitor	F: Ecotin	ECOD (1.6)
G	Ecotin	e4niyG1	A: beta sandwiches	X: Ecotin, trypsin inhibitor (From Topology)	H: Ecotin, trypsin inhibitor (From Topology)	T: Ecotin, trypsin inhibitor	F: Ecotin	ECOD (1.6)
H	Ecotin	e4niyH1	A: beta sandwiches	X: Ecotin, trypsin inhibitor (From Topology)	H: Ecotin, trypsin inhibitor (From Topology)	T: Ecotin, trypsin inhibitor	F: Ecotin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
C	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
D	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
E	2.60.40.550	Mainly Beta	Sandwich	Immunoglobulin-like	Ecotin	CATH (4.3.0)
F	2.60.40.550	Mainly Beta	Sandwich	Immunoglobulin-like	Ecotin	CATH (4.3.0)
G	2.60.40.550	Mainly Beta	Sandwich	Immunoglobulin-like	Ecotin	CATH (4.3.0)
H	2.60.40.550	Mainly Beta	Sandwich	Immunoglobulin-like	Ecotin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00089	Trypsin (Trypsin)	Trypsin		Domain
E, F, G, H	PF03974	Ecotin (Ecotin)	Ecotin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cationic trypsin	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity protein binding binding serpin family protein binding cation binding ion binding metal ion binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity protein binding binding serpin family protein binding cation binding ion binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal process digestion	protein-containing complex serine protease inhibitor complex protease inhibitor complex peptidase inhibitor complex cellular anatomical structure extracellular region extracellular space
E, F, G, H	Ecotin	enzyme regulator activity molecular function inhibitor activity peptidase regulator activity serine-type endopeptidase inhibitor activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	response to stimulus defense response response to stress	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D	IPR001314	Peptidase S1A, chymotrypsin family	Family
A, B, C, D	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A, B, C, D	IPR001254	Serine proteases, trypsin domain	Domain
A, B, C, D	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B, C, D	IPR050127	Serine Proteases (Peptidase S1 Family)	Family
A, B, C, D	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
E, F, G, H	IPR005658	Proteinase inhibitor I11, ecotin	Family
E, F, G, H	IPR036198	Ecotin superfamily	Homologous Superfamily
E, F, G, H	IPR023084	Proteinase inhibitor I11, ecotin, gammaproteobacteria	Family
E, F, G, H	IPR027438	Ecotin, C-terminal	Homologous Superfamily

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.