5YD3 | pdb_00005yd3

Crystal structure of the scFv antibody 4B08 with epitope peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Pept_tRNA_hydro	e5yd3A1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Pept_tRNA_hydro	ECOD (develop294)
C	Pept_tRNA_hydro	e5yd3C1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Pept_tRNA_hydro	ECOD (develop294)
E	Pept_tRNA_hydro	e5yd3E1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Pept_tRNA_hydro	ECOD (develop294)
G	Pept_tRNA_hydro	e5yd3G1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Pept_tRNA_hydro	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

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, C, E, G	scFv 4B08	SCFV-HEAVY-KAPPA	Mus musculus (house mouse)	IGHV1-6302, IGHJ401, IGKV2-13701, IGKJ202, IGKJ2*03	V-DOMAIN VH, V-DOMAIN V-KAPPA	IG	SCFV-HEAVY-KAPPA	IMGT (202610-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	scFv 4B08	binding antigen binding	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
B, D, F, H	Epitope peptide	protein binding binding virus receptor activity exogenous protein binding molecular transducer activity coreceptor activity signaling receptor activity phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity glycerophospholipase activity hydrolase activity C-type glycerophospholipase activity protein binding binding virus receptor activity exogenous protein binding molecular transducer activity coreceptor activity signaling receptor activity phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity glycerophospholipase activity hydrolase activity C-type glycerophospholipase activity phosphatidylinositol-4,5-bisphosphate phospholipase C activity catalytic activity lipase activity G protein-coupled chemoattractant receptor activity C-C chemokine receptor activity chemokine receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity cytokine receptor activity immune receptor activity cytoskeletal protein binding actin binding C-C chemokine binding chemokine binding cytokine binding chemokine (C-C motif) ligand 5 binding identical protein binding	regulation of cellular process leukocyte apoptotic process negative regulation of biological process regulation of programmed cell death macrophage apoptotic process negative regulation of leukocyte apoptotic process negative regulation of cellular process myeloid cell apoptotic process regulation of leukocyte apoptotic process regulation of biological process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of macrophage apoptotic process regulation of cellular process leukocyte apoptotic process negative regulation of biological process regulation of programmed cell death macrophage apoptotic process negative regulation of leukocyte apoptotic process negative regulation of cellular process myeloid cell apoptotic process regulation of leukocyte apoptotic process regulation of biological process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of macrophage apoptotic process cell death negative regulation of apoptotic process regulation of macrophage apoptotic process inflammatory cell apoptotic process cellular process negative regulation of myeloid cell apoptotic process apoptotic process regulation of myeloid cell apoptotic process programmed cell death positive regulation of cytosolic calcium ion concentration regulation of biological quality response to stimulus immune response immune system process response to sterol response to lipid response to alcohol response to chemical response to oxygen-containing compound response to cholesterol signaling cell-cell signaling cell communication cellular response to stimulus biological process involved in interspecies interaction between organisms response to other organism cellular response to lipopolysaccharide response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin intracellular signal transduction calcium-mediated signaling intracellular signaling cassette signal transduction MAPK cascade chemotaxis taxis locomotion cell chemotaxis dendritic cell chemotaxis leukocyte migration dendritic cell migration mononuclear cell migration cell migration cell motility leukocyte chemotaxis cell surface receptor signaling pathway defense response response to stress cellular defense response localization transport monoatomic ion transport monoatomic cation transport establishment of localization calcium ion transport metal ion transport inflammatory response G protein-coupled receptor signaling pathway release of sequestered calcium ion into cytosol by endoplasmic reticulum calcium ion transmembrane import into cytosol monoatomic ion transmembrane transport sarcoplasmic reticulum calcium ion transport release of sequestered calcium ion into cytosol by sarcoplasmic reticulum monoatomic cation transmembrane transport transmembrane transport release of sequestered calcium ion into cytosol calcium ion transmembrane transport	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR050150	Immunoglobulin Variable Light Chain	Family
A, C, E, G	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C, E, G	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR013106	Immunoglobulin V-set domain	Domain
A, C, E, G	IPR003599	Immunoglobulin domain subtype	Domain
A, C, E, G	IPR007110	Immunoglobulin-like domain	Domain
B, D, F, H	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
B, D, F, H	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
B, D, F, H	IPR000355	Chemokine receptor family	Family
B, D, F, H	IPR050119	C-C chemokine receptor type 1-9-like	Family
B, D, F, H	IPR002240	CC chemokine receptor 5	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H	Pharos: P51681	hepatitis C virus infection type 1 diabetes mellitus 22 nephritis West Nile fever inflammatory bowel disease Kidney Failure, Acute acquired metabolic disease psoriasis schizophrenia autoimmune disease tuberculosis celiac disease ulcerative colitis dermatitis, atopic glioblastoma hepatitis C virus infection type 1 diabetes mellitus 22 nephritis West Nile fever inflammatory bowel disease Kidney Failure, Acute acquired metabolic disease psoriasis schizophrenia autoimmune disease tuberculosis celiac disease ulcerative colitis dermatitis, atopic glioblastoma hepatocellular carcinoma interstitial cystitis lung cancer osteosarcoma acute kidney failure rheumatoid arthritis AIDS Sjogren syndrome cancer type 1 diabetes mellitus chronic obstructive pulmonary disease diabetes mellitus head and neck cancer IgA glomerulonephritis invasive ductal breast carcinoma malignant glioma pilocytic astrocytoma sarcoidosis atopic eczema subependymal giant cell astrocytoma cutaneous lupus erythematosus West-Nile encephalitis ductal breast carcinoma in situ

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.