4LVO

Crystal structure of PfSUB1-prodomain-NIMP.M7 Fab complex with added CaCl2

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)
B	d4lvob2	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	d4lvob1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4lvoc1	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	d4lvoc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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	SCOP2B Superfamily	Subtilisin-like	8098196	3000226	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_S8	e4lvoA1	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like (From Topology)	T: Subtilisin-like	F: Peptidase_S8	ECOD (1.6)
B	C1-set_4	e4lvoB1	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	e4lvoB2	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)
C	V-set_8	e4lvoC2	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	e4lvoC1	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	e4lvoP1	A: a+b two layers	X: Alpha-beta plaits	H: Protease propeptides/inhibitors (From Topology)	T: Protease propeptides/inhibitors	F: PTZ00262	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)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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)

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
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 (202436-0)
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 (202436-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Light Chain	IGKV4	Kappa	subtilisin-like serine protease	SAbDab (2024-09-13)
C	Heavy Chain	IGHV3	-	subtilisin-like serine protease	SAbDab (2024-09-13)

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

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	peptide hormone processing organonitrogen compound metabolic process cellular biosynthetic process regulation of hormone levels cellular metabolic process biological regulation signaling receptor ligand precursor processing primary metabolic process gene expression macromolecule biosynthetic process hormone metabolic process protein maturation biosynthetic process proteolysis peptide hormone processing organonitrogen compound metabolic process cellular biosynthetic process regulation of hormone levels cellular metabolic process biological regulation signaling receptor ligand precursor processing primary metabolic process gene expression macromolecule biosynthetic process hormone metabolic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process amide metabolic process protein metabolic process macromolecule metabolic process regulation of biological quality	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm extracellular region membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm extracellular region extracellular space cell projection neuron projection plasma membrane bounded cell projection
B	NIMP.M7 Fab light chain	-	-	-
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	peptide hormone processing organonitrogen compound metabolic process cellular biosynthetic process regulation of hormone levels cellular metabolic process biological regulation signaling receptor ligand precursor processing primary metabolic process gene expression macromolecule biosynthetic process hormone metabolic process protein maturation biosynthetic process proteolysis peptide hormone processing organonitrogen compound metabolic process cellular biosynthetic process regulation of hormone levels cellular metabolic process biological regulation signaling receptor ligand precursor processing primary metabolic process gene expression macromolecule biosynthetic process hormone metabolic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process amide metabolic process protein metabolic process macromolecule metabolic process regulation of biological quality	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm extracellular region membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm extracellular region extracellular space cell projection neuron projection plasma membrane bounded cell projection

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 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 R01GM133198.