2I5Y | pdb_00002i5y

Crystal structure of CD4M47, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 GP120 envelope glycoprotein and anti-HIV-1 antibody 17B

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth S]	d2i5ys1	Designed proteins	Scorpion toxin-based designs	Scorpion toxin-based designs	Mini-protein reproducing the core of the CD4 surface	Mini-protein reproducing the core of the CD4 surface	(synthetic construct ) [TaxId: 32630 ],	SCOPe (2.08)
D [auth M]	d2i5ym1	Designed proteins	Scorpion toxin-based designs	Scorpion toxin-based designs	Mini-protein reproducing the core of the CD4 surface	Mini-protein reproducing the core of the CD4 surface	(synthetic construct ) [TaxId: 32630 ],	SCOPe (2.08)
G [auth R]	d2i5yr1	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)
G [auth R]	d2i5yr2	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 [auth H]	d2i5yh1	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)
C [auth H]	d2i5yh2	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)
F [auth Q]	d2i5yq1	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)
F [auth Q]	d2i5yq2	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 [auth L]	d2i5yl1	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)
B [auth L]	d2i5yl2	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)
E [auth P]	d2i5yp2	Alpha and beta proteins (a+b)	gp120 core	gp120 core	gp120 core	gp120 core	(Human immunodeficiency virus ) [TaxId: 12721 ], (Human immunodeficiency virus ) [TaxId: 12721 ], (Human immunodeficiency virus ) [TaxId: 12721 ],	SCOPe (2.08)
E [auth P]	d2i5yp3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus ) [TaxId: 12721 ], (Human immunodeficiency virus ) [TaxId: 12721 ], (Human immunodeficiency virus ) [TaxId: 12721 ],	SCOPe (2.08)
A [auth G]	d2i5yg2	Alpha and beta proteins (a+b)	gp120 core	gp120 core	gp120 core	gp120 core	(Human immunodeficiency virus ) [TaxId: 12721 ], (Human immunodeficiency virus ) [TaxId: 12721 ], (Human immunodeficiency virus ) [TaxId: 12721 ],	SCOPe (2.08)
A [auth G]	d2i5yg3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus ) [TaxId: 12721 ], (Human immunodeficiency virus ) [TaxId: 12721 ], (Human immunodeficiency virus ) [TaxId: 12721 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth H]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091519	3000071	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)
H [auth S]	MarR	e2i5yS1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: MarR	ECOD (develop294)
G [auth R]	Copper-bind	e2i5yR1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
C [auth H]	Copper-bind	e2i5yH1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
F [auth Q]	Copper-bind	e2i5yQ1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
B [auth L]	Copper-bind	e2i5yL1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
E [auth P]	GP120	e2i5yP1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GP120	ECOD (develop294)
A [auth G]	GP120	e2i5yG1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GP120	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth R]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth Q]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth P]	2.170.40.20	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120	Chain G	CATH (4.3.0)
A [auth G]	2.170.40.20	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120	Chain G	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 H], G [auth R]	17B mAb, anti-gp120 [HIV-1]; CD4M47, scorpion toxic mimic of CD4	VH-CH1	Homo sapiens (human)	IGHV1-6902, IGHV1-6904, IGHV1-6908, IGHV1-6909, IGHJ501, IGHJ502, IGHG101, IGHG102, IGHG1*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
B [auth L], F [auth Q]	17B mAb, anti-gp120 [HIV-1]; CD4M47, scorpion toxic mimic of CD4	L-KAPPA	Homo sapiens (human)	IGKV3-1501, IGKV3D-1501, IGKJ501, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], G [auth R]	Heavy Chain	IGHV1	-	exterior membrane glycoprotein(gp120)	SAbDab (2026-03-20)
B [auth L], F [auth Q]	Light Chain	IGKV3	Kappa	exterior membrane glycoprotein(gp120)	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth H], G [auth R]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth M], H [auth S]	CD4M47, SCORPION-TOXIN MIMIC OF CD4	-	-	-
C [auth H], G [auth R]	Antibody 17B Heavy chain	protein-containing complex binding protein binding binding signaling receptor binding immunoglobulin receptor binding Fc-gamma receptor I complex binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress leukocyte mediated immunity antibody-dependent cellular cytotoxicity acute inflammatory response hypersensitivity defense response immune response leukocyte mediated cytotoxicity acute inflammatory response to antigenic stimulus adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress leukocyte mediated immunity antibody-dependent cellular cytotoxicity acute inflammatory response hypersensitivity defense response immune response leukocyte mediated cytotoxicity acute inflammatory response to antigenic stimulus immunoglobulin mediated immune response adaptive immune response immune effector process type II hypersensitivity immune system process type IIa hypersensitivity B cell mediated immunity cellular process inflammatory response cell killing cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin complement activation, classical pathway complement-dependent cytotoxicity biological process involved in interspecies interaction between organisms response to other organism 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 bacterium response to external biotic stimulus	cellular anatomical structure extracellular region extracellular space blood microparticle protein-containing complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cellular anatomical structure extracellular region extracellular space blood microparticle protein-containing complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex
B [auth L], F [auth Q]	Antibody 17B Light chain	-	-	-
A [auth G], E [auth P]	Exterior membrane glycoprotein(GP120)	structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of receptor clustering biological regulation positive regulation of biological process positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization macromolecule localization receptor clustering positive regulation of protein localization intracellular protein localization regulation of receptor clustering regulation of protein localization to membrane positive regulation of cellular process virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction plasma membrane raft distribution regulation of cellular component organization positive regulation of cellular component organization plasma membrane raft polarization plasma membrane organization membrane raft organization endomembrane system organization membrane raft distribution plasma membrane raft localization membrane raft polarization regulation of plasma membrane raft polarization membrane raft localization regulation of plasma membrane organization positive regulation of plasma membrane raft polarization import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral protein processing symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region viral membrane viral envelope host cell plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth H], G [auth R]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth H], G [auth R]	IPR050380	Immune Recognition and Response Modulators	Family
C [auth H], G [auth R]	IPR003597	Immunoglobulin C1-set	Domain
C [auth H], G [auth R]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth H], G [auth R]	IPR007110	Immunoglobulin-like domain	Domain
C [auth H], G [auth R]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C [auth H], G [auth R]	IPR003597	Immunoglobulin C1-set	Domain
C [auth H], G [auth R]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth H], G [auth R]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth H], G [auth R]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth H], G [auth R]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth H], G [auth R]	IPR007110	Immunoglobulin-like domain	Domain
C [auth H], G [auth R]	IPR050380	Immune Recognition and Response Modulators	Family
C [auth H], G [auth R]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth G], E [auth P]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A [auth G], E [auth P]	IPR036377	Gp120 core superfamily	Homologous Superfamily
A [auth G], E [auth P]	IPR000328	Retroviral envelope protein GP41-like	Domain
A [auth G], E [auth P]	IPR037527	Envelope glycoprotein Gp160	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth H], G [auth R]	Pharos: P01857	B-cell chronic lymphocytic leukemia myositis polycystic ovary syndrome plasma cell myeloma plasma cell neoplasm Sclerocystic Ovaries acquired idiopathic inflammatory myopathy lung adenocarcinoma ovarian cancer peripheral neuropathy Sjogren syndrome amyloidosis breast cancer medulloblastoma nasopharyngeal carcinoma B-cell chronic lymphocytic leukemia myositis polycystic ovary syndrome plasma cell myeloma plasma cell neoplasm Sclerocystic Ovaries acquired idiopathic inflammatory myopathy lung adenocarcinoma ovarian cancer peripheral neuropathy Sjogren syndrome amyloidosis breast cancer medulloblastoma nasopharyngeal carcinoma periodontitis interstitial cystitis myeloid neoplasm osteosarcoma peripheral nervous system disease

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.