5E5M

Crystal structure of mouse CTLA-4 in complex with nanobody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5e5ma_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoreceptor CTLA-4 (CD152), N-terminal fragment	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d5e5mc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoreceptor CTLA-4 (CD152), N-terminal fragment	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d5e5me_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoreceptor CTLA-4 (CD152), N-terminal fragment	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d5e5mg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoreceptor CTLA-4 (CD152), N-terminal fragment	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d5e5mf_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Camelidae ) [TaxId: 9835 ],	SCOPe (2.08)
H	d5e5mh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Camelidae ) [TaxId: 9835 ],	SCOPe (2.08)
B	d5e5mb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Camelidae ) [TaxId: 9835 ],	SCOPe (2.08)
D	d5e5md_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Camelidae ) [TaxId: 9835 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054467	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054467	3000071	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054467	3000071	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054467	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)
A	V-set_6	e5e5mA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_6	ECOD (1.6)
C	V-set_6	e5e5mC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_6	ECOD (1.6)
E	V-set_6	e5e5mE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_6	ECOD (1.6)
G	V-set_6	e5e5mG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_6	ECOD (1.6)
F	V-set_10	e5e5mF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
H	V-set_10	e5e5mH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
B	V-set_8	e5e5mB1	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)
D	V-set_10	e5e5mD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	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)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	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)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D, F, H	Heavy Chain	IGHV1	-	cytotoxic t-lymphocyte protein 4	SAbDab (2025-02-21)

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	Cytotoxic T-lymphocyte protein 4	-	response to stimulus immune response immune system process adaptive immune response multicellular organismal process regulation of cellular process regulation of leukocyte activation regulation of cell activation lymphocyte activation leukocyte proliferation leukocyte activation T cell activation lymphocyte proliferation regulation of immune system process response to stimulus immune response immune system process adaptive immune response multicellular organismal process regulation of cellular process regulation of leukocyte activation regulation of cell activation lymphocyte activation leukocyte proliferation leukocyte activation T cell activation lymphocyte proliferation regulation of immune system process regulation of multicellular organismal process T cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation regulation of biological process cell population proliferation biological regulation cell activation regulation of T cell activation regulation of T cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of mononuclear cell proliferation cellular process regulation of lymphocyte activation	cell periphery cellular anatomical structure plasma membrane membrane cell surface external side of plasma membrane side of membrane protein-containing complex protein complex involved in cell adhesion
B, D, F, H	CTLA-4 nanobody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR040216	Cytotoxic T-lymphocyte protein 4/CD28	Family
A, C, E, G	IPR008096	Cytotoxic T-lymphocyte antigen 4	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

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.