5F72

De novo design and crystallographic validation of antibodies targeting a pre-selected epitope

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth S]	d5f72s_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth T]	d5f72t_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth K]	SCOP2B Superfamily	Kelch motif	8033525	3000448	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Kelch motif	8033525	3000448	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 [auth K]	PF01344	e5f72K1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: PF01344	ECOD (1.6)
B [auth C]	PF01344	e5f72C1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: PF01344	ECOD (1.6)
D [auth S]	PF07686	e5f72S2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth T]	PF07686	e5f72T1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth K]	2.120.10.80	Mainly Beta	6 Propeller	Neuraminidase	Kelch-type beta propeller	CATH (4.3.0)
B [auth C]	2.120.10.80	Mainly Beta	6 Propeller	Neuraminidase	Kelch-type beta propeller	CATH (4.3.0)
D [auth S]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth T]	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 [auth T], D [auth S]	Single chain Fv from a Fab	SCFV-HEAVY-KAPPA	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ301, IGHJ501, IGHJ502, IGKV1-3901, IGKV1D-3901, IGKJ101, IGKJ401, IGKJ4*02	V-DOMAIN VH, V-DOMAIN V-KAPPA	IG	SCFV-HEAVY-KAPPA	IMGT (202416-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth K], B [auth C]	PF01344	Kelch motif (Kelch_1)	Kelch motif	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth K], B [auth C]	Kelch-like ECH-associated protein 1	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity disordered domain specific binding protein domain specific binding identical protein binding	developmental process multicellular organismal process epithelium development regulation of biological process regulation of multicellular organismal development regulation of cellular process cellular developmental process regulation of developmental process epidermal cell differentiation regulation of epidermal cell differentiation epidermis development biological regulation regulation of cell differentiation tissue development epithelial cell differentiation developmental process multicellular organismal process epithelium development regulation of biological process regulation of multicellular organismal development regulation of cellular process cellular developmental process regulation of developmental process epidermal cell differentiation regulation of epidermal cell differentiation epidermis development biological regulation regulation of cell differentiation tissue development epithelial cell differentiation regulation of epithelial cell differentiation multicellular organism development cell differentiation anatomical structure development cellular process regulation of multicellular organismal process regulation of epidermis development cellular biosynthetic process negative regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process negative regulation of molecular function primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of molecular function organic cyclic compound metabolic process regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to organic substance response to stimulus response to cytokine response to interleukin-4 cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to interleukin-4 cellular response to organic substance positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of protein catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal response to oxidative stress cellular response to stress response to stress cellular response to oxidative stress cellular response to chemical stress embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development autophagy regulation of autophagy cellular catabolic process regulation of cellular catabolic process process utilizing autophagic mechanism	midbody cellular anatomical entity intracellular anatomical structure intracellular organelle centrosome microtubule organizing center cytoskeleton centriolar satellite organelle intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol midbody cellular anatomical entity intracellular anatomical structure intracellular organelle centrosome microtubule organizing center cytoskeleton centriolar satellite organelle intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol inclusion body membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen polymeric cytoskeletal fiber actin filament actin cytoskeleton supramolecular fiber supramolecular polymer supramolecular complex cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex Cul3-RING ubiquitin ligase complex intracellular protein-containing complex endoplasmic reticulum endomembrane system
C [auth T], D [auth S]	Single chain Fv from a Fab	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth K], B [auth C]	IPR000210	BTB/POZ domain	Domain
A [auth K], B [auth C]	IPR015915	Kelch-type beta propeller	Homologous Superfamily
A [auth K], B [auth C]	IPR006652	Kelch repeat type 1	Repeat
A [auth K], B [auth C]	IPR011705	BTB/Kelch-associated	Domain
A [auth K], B [auth C]	IPR017096	BTB-kelch protein	Family
A [auth K], B [auth C]	IPR030563	Kelch-like ECH-associated protein 1, BTB/POZ domain	Domain
A [auth K], B [auth C]	IPR047098	Kelch-like ECH-associated protein 1, BACK domain	Domain
A [auth K], B [auth C]	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth K], B [auth C]	Pharos: Q14145	renal cell carcinoma keratosis lung cancer non-small cell lung carcinoma collecting duct carcinoma gallbladder cancer chromophobe renal cell carcinoma sarcomatoid renal cell carcinoma hepatitis papillary renal cell carcinoma prostate cancer Hepatomegaly ankylosing spondylitis digestive system disease inflammatory bowel disease renal cell carcinoma keratosis lung cancer non-small cell lung carcinoma collecting duct carcinoma gallbladder cancer chromophobe renal cell carcinoma sarcomatoid renal cell carcinoma hepatitis papillary renal cell carcinoma prostate cancer Hepatomegaly ankylosing spondylitis digestive system disease inflammatory bowel disease lung disease osteosarcoma astrocytic tumor primary biliary cholangitis relapsing-remitting multiple sclerosis extrahepatic cholestasis gallbladder neoplasm lung adenocarcinoma cancer clear cell renal carcinoma renal carcinoma Crohn disease

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.