4LVN

Crystal structure of PfSUB1-prodomain-NIMP.M7 Fab complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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)
C	d4lvnc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4lvnc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d4lvnb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d4lvnb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Subtilases	8098195	4000409	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Subtilisin-like	8098196	3000226	SCOP2 (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_S8	e4lvnA1	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like (From Topology)	T: Subtilisin-like	F: Peptidase_S8	ECOD (1.6)
C	V-set_8	e4lvnC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C	C1-set_1	e4lvnC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D [auth P]	PTZ00262	e4lvnP1	A: a+b two layers	X: Alpha-beta plaits	H: Protease propeptides/inhibitors (From Topology)	T: Protease propeptides/inhibitors	F: PTZ00262	ECOD (1.6)
B	C1-set_4	e4lvnB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e4lvnB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.200	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Peptidase S8/S53 domain	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth P]	3.30.70.2380	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C	NIMP.M7 FAB HEAVY CHAIN	VH-CH1	Mus musculus (house mouse)	IGHV3-102, IGHJ101, IGHJ102, IGHG101, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B	NIMP.M7 FAB HEAVY CHAIN	L-KAPPA	Mus musculus (house mouse)	IGKV4-7401, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Heavy Chain	IGHV3	-	subtilisin-like serine protease	SAbDab (2024-04-19)
B	Light Chain	IGKV4	Kappa	subtilisin-like serine protease	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00082	Subtilase family (Peptidase_S8)	Subtilase family	Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see Pfam:PF00089). Structure is an alpha/beta fold containing a 7 ...	Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see Pfam:PF00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.	Domain
D [auth P]	PF18213	SUB1 protease Prodomain ProdP9 (SUB1_ProdP9)	SUB1 protease Prodomain ProdP9	This domain is the bound prodomain fragment ProdP9 of the SUB1 protein present in Plasmodium falciparum. SUB1 is a serine protease that processes a subset of parasite proteins that play indispensable roles in egress and invasion. The C-terminal stal ...	This domain is the bound prodomain fragment ProdP9 of the SUB1 protein present in Plasmodium falciparum. SUB1 is a serine protease that processes a subset of parasite proteins that play indispensable roles in egress and invasion. The C-terminal stalk of ProdP9 binds in the active site groove in a substrate-like manner and is truncated at the N terminus as a result of the chymotrypsin digestion step used during purification. ProdP9 is structural similar to MIC5 from Toxoplasma gondii, despite low sequence identity [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Subtilisin-like serine protease	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity cation binding ion binding binding metal ion binding small molecule binding	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region cellular anatomical entity
C	NIMP.M7 Fab heavy chain	-	-	-
D [auth P]	Subtilisin-like serine protease	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity cation binding ion binding binding metal ion binding small molecule binding	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region cellular anatomical entity
B	NIMP.M7 Fab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023828	Peptidase S8, subtilisin, Ser-active site	Active Site
A	IPR022398	Peptidase S8, subtilisin, His-active site	Active Site
A	IPR000209	Peptidase S8/S53 domain	Domain
A	IPR041089	SUB1 protease prodomain ProdP9	Domain
A	IPR015500	Peptidase S8, subtilisin-related	Family
A	IPR036852	Peptidase S8/S53 domain superfamily	Homologous Superfamily
A	IPR017314	Peptidase S8A, subtilisin-like peptidase 1, plasmodium	Family
A	IPR023827	Peptidase S8, subtilisin, Asp-active site	Active Site
A	IPR034204	Subtilisin SUB1-like catalytic domain	Domain
D [auth P]	IPR023828	Peptidase S8, subtilisin, Ser-active site	Active Site
D [auth P]	IPR022398	Peptidase S8, subtilisin, His-active site	Active Site
D [auth P]	IPR000209	Peptidase S8/S53 domain	Domain
D [auth P]	IPR041089	SUB1 protease prodomain ProdP9	Domain
D [auth P]	IPR015500	Peptidase S8, subtilisin-related	Family
D [auth P]	IPR036852	Peptidase S8/S53 domain superfamily	Homologous Superfamily
D [auth P]	IPR017314	Peptidase S8A, subtilisin-like peptidase 1, plasmodium	Family
D [auth P]	IPR023827	Peptidase S8, subtilisin, Asp-active site	Active Site
D [auth P]	IPR034204	Subtilisin SUB1-like catalytic domain	Domain

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.