7JTI

Interphotoreceptor retinoid-binding protein (IRBP) in complex with a monoclonal antibody (F3F5 mAb5)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2 Family	Tail specific protease, catalytic domain	8098491	4003564	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	ClpP/crotonase	8098492	3000033	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 [auth L]	C1-set	e7jtiL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
A [auth L]	V-set_3	e7jtiL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
B [auth H]	V-set_8	e7jtiH2	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)
B [auth H]	C1-set_1	e7jtiH1	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)
C [auth A]	Peptidase_S41_N	e7jtiA2	A: alpha bundles	X: Tail specific protease helical domain (From Topology)	H: Tail specific protease helical domain (From Topology)	T: Tail specific protease helical domain	F: Peptidase_S41_N	ECOD (1.6)
C [auth A]	Peptidase_S41	e7jtiA1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Peptidase_S41	ECOD (1.6)
D [auth B]	Peptidase_S41_N	e7jtiB2	A: alpha bundles	X: Tail specific protease helical domain (From Topology)	H: Tail specific protease helical domain (From Topology)	T: Tail specific protease helical domain	F: Peptidase_S41_N	ECOD (1.6)
D [auth B]	Peptidase_S41	e7jtiB1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Peptidase_S41	ECOD (1.6)
E [auth C]	Peptidase_S41_N	e7jtiC2	A: alpha bundles	X: Tail specific protease helical domain (From Topology)	H: Tail specific protease helical domain (From Topology)	T: Tail specific protease helical domain	F: Peptidase_S41_N	ECOD (1.6)
E [auth C]	Peptidase_S41	e7jtiC1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Peptidase_S41	ECOD (1.6)
F [auth D]	Peptidase_S41_N	e7jtiD2	A: alpha bundles	X: Tail specific protease helical domain (From Topology)	H: Tail specific protease helical domain (From Topology)	T: Tail specific protease helical domain	F: Peptidase_S41_N	ECOD (1.6)
F [auth D]	Peptidase_S41	e7jtiD1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Peptidase_S41	ECOD (1.6)

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
A [auth L]	Fab mAb5	L-LAMBDA	Bos taurus (bovine)	IGLV101, IGLJ302, IGLJ101, IGLC101	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202438-0)
B [auth H]	Fab mAb5	VH-CH1	Bos taurus (bovine)	IGHV2-902, IGHJ401, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202438-0)
C [auth A]	Retinol-binding protein 3 (Pr633-932) (P12661)	null	Bos taurus (bovine)	-	-	TR	Protein	IMGT (202438-0)
D [auth B]	Retinol-binding protein 3 (Pr633-932) (P12661)	null	Bos taurus (bovine)	-	-	TR	Protein	IMGT (202438-0)
F [auth D]	Retinol-binding protein 3 (Pr633-932) (P12661)	null	-	-	-	TR	Protein	IMGT (202438-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGLV1	Lambda	retinol-binding protein 3	SAbDab (2024-09-27)
B [auth H]	Heavy Chain	IGHV2	-	retinol-binding protein 3	SAbDab (2024-09-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF03572	Peptidase family S41 (Peptidase_S41)	Peptidase family S41	-	Family
C [auth A]	PF11918	N-terminal domain of Peptidase_S41 in eukaryotic IRBP (Peptidase_S41_N)	N-terminal domain of Peptidase_S41 in eukaryotic IRBP	Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterise ...	Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterised as a serine-peptidase, Pfam:PF03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B [1].	Domain
D [auth B]	PF03572	Peptidase family S41 (Peptidase_S41)	Peptidase family S41	-	Family
D [auth B]	PF11918	N-terminal domain of Peptidase_S41 in eukaryotic IRBP (Peptidase_S41_N)	N-terminal domain of Peptidase_S41 in eukaryotic IRBP	Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterise ...	Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterised as a serine-peptidase, Pfam:PF03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B [1].	Domain
E [auth C]	PF03572	Peptidase family S41 (Peptidase_S41)	Peptidase family S41	-	Family
E [auth C]	PF11918	N-terminal domain of Peptidase_S41 in eukaryotic IRBP (Peptidase_S41_N)	N-terminal domain of Peptidase_S41 in eukaryotic IRBP	Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterise ...	Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterised as a serine-peptidase, Pfam:PF03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B [1].	Domain
F [auth D]	PF03572	Peptidase family S41 (Peptidase_S41)	Peptidase family S41	-	Family
F [auth D]	PF11918	N-terminal domain of Peptidase_S41 in eukaryotic IRBP (Peptidase_S41_N)	N-terminal domain of Peptidase_S41 in eukaryotic IRBP	Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterise ...	Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterised as a serine-peptidase, Pfam:PF03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L]	mAb5 Fab light chain	-	-	-
B [auth H]	mAb5 Fab heavy chain	-	-	-
C [auth A]	Retinol-binding protein 3	vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity	proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region cellular anatomical entity cell periphery cone matrix sheath extracellular matrix external encapsulating structure interphotoreceptor matrix collagen-containing extracellular matrix
D [auth B]	Retinol-binding protein 3	vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity all-trans-retinol binding fatty acid binding organic acid binding long-chain fatty acid binding oleic acid binding ion binding anion binding carboxylic acid binding monocarboxylic acid binding	proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	-
E [auth C]	Retinol-binding protein 3	vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity	proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region cellular anatomical entity cell periphery cone matrix sheath extracellular matrix external encapsulating structure interphotoreceptor matrix collagen-containing extracellular matrix
F [auth D]	Retinol-binding protein 3	vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity	proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region cellular anatomical entity cell periphery cone matrix sheath extracellular matrix external encapsulating structure interphotoreceptor matrix collagen-containing extracellular matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR005151	Tail specific protease	Domain
C [auth A]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
D [auth B]	IPR005151	Tail specific protease	Domain
D [auth B]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
E [auth C]	IPR005151	Tail specific protease	Domain
E [auth C]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
F [auth D]	IPR005151	Tail specific protease	Domain
F [auth D]	IPR029045	ClpP/crotonase-like domain superfamily	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.