1H0D

Crystal structure of Human Angiogenin in complex with Fab fragment of its monoclonal antibody mAb 26-2F

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
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1h0da1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1h0da2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1h0db1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1h0db2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1h0dc_	Alpha and beta proteins (a+b)	RNase A-like	RNase A-like	Ribonuclease A-like	Angiogenin	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)
C	SCOP2B Superfamily	RNase A-like	8040055	3001918	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	PF07654	e1h0dA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A	PF07686	e1h0dA1	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)
B	PF07654	e1h0dB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B	PF07686	e1h0dB1	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	PF00074	e1h0dC1	A: a+b complex topology	X: RNase A-like	H: RNase A-like (From Topology)	T: RNase A-like	F: PF00074	ECOD (1.6)

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 (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	3.10.130.10	Alpha Beta	Roll	P-30 Protein	Ribonuclease A-like domain	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
A	26-2F mAb, anti-angiogenin	L-KAPPA	Mus musculus (house mouse)	IGKV3-201, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
B	26-2F mAb, anti-angiogenin	VH-CH1	Mus musculus (house mouse)	IGHV5-901, IGHV5-903, IGHV5-9-501, IGHJ401, IGHG101, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A	Light Chain	IGKV3	Kappa	angiogenin	SAbDab (2024-04-26)
B	Heavy Chain	IGHV5	-	angiogenin	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00074	Pancreatic ribonuclease (RnaseA)	Pancreatic ribonuclease	Ribonucleases. Members include pancreatic RNAase A and angiogenins. Structure is an alpha+beta fold -- long curved beta sheet and three helices.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ANTIBODY FAB FRAGMENT, LIGHT CHAIN	-	-	-
B	ANTIBODY FAB FRAGMENT, HEAVY CHAIN	-	-	-
C	ANGIOGENIN	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding cation binding transition metal ion binding copper ion binding ion binding metal ion binding small molecule binding DNA binding endonuclease activity nuclease activity RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding cation binding transition metal ion binding copper ion binding ion binding metal ion binding small molecule binding DNA binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity protein binding signaling receptor binding identical protein binding protein homodimerization activity protein dimerization activity cytoskeletal protein binding actin binding peptide binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process placenta development animal organ development anatomical structure development regulation of cellular process positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process developmental process placenta development animal organ development anatomical structure development regulation of cellular process positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation regulation of biological process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of molecular function positive regulation of protein modification process organic substance metabolic process protein metabolic process activation of protein kinase B activity positive regulation of protein kinase activity positive regulation of cellular process organonitrogen compound metabolic process positive regulation of transferase activity biological regulation positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of phosphorylation cellular process humoral immune response biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response immune response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress immune system process response to bacterium response to external biotic stimulus innate immune response cell migration cell motility sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction female gamete generation gamete generation oocyte development anatomical structure maturation cell differentiation germ cell development oocyte maturation oocyte differentiation cell maturation multicellular organismal process gonad development reproductive system development female gonad development sex differentiation female sex differentiation development of primary female sexual characteristics multicellular organism development development of primary sexual characteristics reproductive structure development ovarian follicle development system development cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process organic cyclic compound biosynthetic process response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus regulation of phospholipase activity positive regulation of phospholipase activity positive regulation of phospholipase C activity positive regulation of lipase activity positive regulation of hydrolase activity regulation of phospholipase C activity regulation of hydrolase activity regulation of lipase activity activation of phospholipase C activity response to organic substance response to hormone response to chemical response to endogenous stimulus organonitrogen compound biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process translation negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development protein polymerization actin polymerization or depolymerization actin filament polymerization actin cytoskeleton organization protein-containing complex organization actin filament organization cellular component organization cellular component biogenesis organelle organization cellular component assembly protein-containing complex assembly actin filament-based process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization negative regulation of cell population proliferation cell population proliferation regulation of smooth muscle cell proliferation smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization transport positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport localization regulation of secretion by cell secretion by cell positive regulation of secretion cellular macromolecule localization regulation of transport secretion organic substance transport regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization catabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process tRNA metabolic process nucleic acid catabolic process tRNA decay organic substance catabolic process RNA catabolic process antimicrobial humoral immune response mediated by antimicrobial peptide cell communication neutral lipid metabolic process diacylglycerol biosynthetic process neutral lipid biosynthetic process lipid biosynthetic process acylglycerol biosynthetic process diacylglycerol metabolic process glycerolipid biosynthetic process cellular lipid metabolic process glycerolipid metabolic process acylglycerol metabolic process lipid metabolic process positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation homeostatic process positive regulation of phospholipase A2 activity regulation of phospholipase A2 activity activation of phospholipase A2 activity defense response to Gram-positive bacterium	basement membrane cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm basement membrane cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm cytosol chromosome somatodendritic compartment cell body neuronal cell body extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen protein-containing complex angiogenin-PRI complex growth cone axon cell projection distal axon neuron projection plasma membrane bounded cell projection site of polarized growth cytoplasmic vesicle intracellular vesicle vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR036816	Ribonuclease A-like domain superfamily	Homologous Superfamily
C	IPR001427	Pancreatic ribonuclease	Family
C	IPR023411	Ribonuclease A, active site	Active Site
C	IPR023412	Ribonuclease A-domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P03950	amyotrophic lateral sclerosis type 9 amyotrophic lateral sclerosis Acute-Phase Reaction amyotrophic lateral sclerosis type 1 non-small cell lung carcinoma ovarian cyst pancreatic intraductal papillary-mucinous carcinoma psoriasis breast carcinoma cutaneous lupus erythematosus invasive ductal breast carcinoma malignant colon neoplasm malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm amyotrophic lateral sclerosis type 9 amyotrophic lateral sclerosis Acute-Phase Reaction amyotrophic lateral sclerosis type 1 non-small cell lung carcinoma ovarian cyst pancreatic intraductal papillary-mucinous carcinoma psoriasis breast carcinoma cutaneous lupus erythematosus invasive ductal breast carcinoma malignant colon neoplasm malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm Sjogren syndrome atypical teratoid rhabdoid tumor breast fibroadenoma ductal breast carcinoma in situ lung adenocarcinoma malignant ependymoma neurodegenerative disease ovarian cancer pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer corpus luteum cyst glioblastoma lung cancer malignant glioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.