5XJ3 | pdb_00005xj3

Complex structure of ipilimumab-scFv and CTLA-4

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054465	3000071	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054465	3000071	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054465	3000071	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054465	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)
C	Fam20C	e5xj3C1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Fam20C	ECOD (develop294)
L	TNF	e5xj3L1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
I	TNF	e5xj3I1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
F	TNF	e5xj3F1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
K	TNF	e5xj3K1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
H	TNF	e5xj3H1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
E	TNF	e5xj3E1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
B	TNF	e5xj3B1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
J	TNF	e5xj3J1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
G	TNF	e5xj3G1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
D	TNF	e5xj3D1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (develop294)
A	Fam20C	e5xj3A1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Fam20C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I	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)
K	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)
E	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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E, H, K	Light Chain	IGKV3	Kappa	cytotoxic t-lymphocyte protein 4	SAbDab (2026-03-20)
A, D, G, J	Heavy Chain	IGHV3	-	cytotoxic t-lymphocyte protein 4	SAbDab (2026-03-20)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B, E, H, K	Ipilimumab	CTLA4/CD152, PDCD1/CD279/PD1	Therapeutic SAbDab (2026-03-20)
A, D, G, J	Sovipostobart	CTLA4/CD152, PDCD1/CD279/PD1	Therapeutic SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I, L	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
C, F, I, L	Cytotoxic T-lymphocyte protein 4	molecular sequestering activity receptor decoy activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process negative regulation of lymphocyte proliferation multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process negative regulation of lymphocyte proliferation multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte activation negative regulation of mononuclear cell proliferation negative regulation of leukocyte proliferation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation negative regulation of cellular process regulation of immune system process regulation of multicellular organismal process negative regulation of B cell activation regulation of lymphocyte proliferation regulation of leukocyte proliferation regulation of biological process negative regulation of cell population proliferation cell population proliferation B cell activation biological regulation cell activation B cell proliferation negative regulation of B cell proliferation negative regulation of cell activation negative regulation of immune system process regulation of cell population proliferation mononuclear cell proliferation immune system process regulation of mononuclear cell proliferation negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of lymphocyte activation immune response-regulating cell surface receptor signaling pathway 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 signal transduction positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response T cell receptor signaling pathway negative regulation of signaling regulation of signal transduction regulation of antigen receptor-mediated signaling pathway negative regulation of antigen receptor-mediated signaling pathway negative regulation of cell communication regulation of signaling negative regulation of response to stimulus regulation of T cell receptor signaling pathway negative regulation of signal transduction negative regulation of T cell receptor signaling pathway regulation of cell communication adaptive immune response positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death positive regulation of cellular process negative regulation of T cell proliferation negative regulation of cell adhesion T cell activation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion T cell proliferation regulation of cell adhesion regulation of T cell activation regulation of T cell proliferation regulation of leukocyte differentiation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation regulation of cell development multicellular organism development negative regulation of T cell differentiation cell differentiation anatomical structure development T cell differentiation negative regulation of hemopoiesis developmental process negative regulation of leukocyte differentiation negative regulation of lymphocyte differentiation leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of T cell differentiation negative regulation of regulatory T cell differentiation negative regulation of cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis negative regulation of developmental process regulation of regulatory T cell differentiation negative regulation of cell development regulatory T cell differentiation regulation of hemopoiesis	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system perinuclear region of cytoplasm intracellular vesicle clathrin-coated endocytic vesicle cytoplasmic vesicle clathrin-coated vesicle coated vesicle vesicle endocytic vesicle protein-containing complex protein complex involved in cell adhesion
B, E, H, K	ipilimumab-VL	-	-	-
A, D, G, J	ipilimumab-VH	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L	IPR040216	Cytotoxic T-lymphocyte protein 4/CD28	Family
C, F, I, L	IPR008096	Cytotoxic T-lymphocyte antigen 4	Family
C, F, I, L	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, F, I, L	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, F, I, L	IPR013106	Immunoglobulin V-set domain	Domain
C, F, I, L	IPR003599	Immunoglobulin domain subtype	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F, I, L	Pharos: P16410	Hashimoto thyroiditis rheumatoid arthritis systemic lupus erythematosus oral submucous fibrosis alopecia areata juvenile idiopathic arthritis Graves disease autoimmune lymphoproliferative syndrome due to CTLA4 haploinsuffiency celiac disease melanoma adult T-cell leukemia/lymphoma type 1 diabetes mellitus 12 granulomatosis with polyangiitis peripheral nervous system disease graft versus host disease Hashimoto thyroiditis rheumatoid arthritis systemic lupus erythematosus oral submucous fibrosis alopecia areata juvenile idiopathic arthritis Graves disease autoimmune lymphoproliferative syndrome due to CTLA4 haploinsuffiency celiac disease melanoma adult T-cell leukemia/lymphoma type 1 diabetes mellitus 12 granulomatosis with polyangiitis peripheral nervous system disease graft versus host disease mycosis fungoides peripheral neuropathy primary cutaneous T-cell non-Hodgkin lymphoma Sezary syndrome vitiligo cutaneous lupus erythematosus Lymphoma, T-Cell, Cutaneous diabetes mellitus malignant pleural mesothelioma gastric cancer acquired metabolic disease ovarian disease HIV infectious disease primary biliary cholangitis autoimmune disease interstitial cystitis prostate disease B-cell chronic lymphocytic leukemia breast cancer kidney disease Sjogren syndrome lung cancer ulcerative colitis colitis cutaneous melanoma major depressive disorder gastric carcinoma myasthenia gravis granulomatous slack skin disease osteosarcoma acute T cell leukemia head and neck cancer arthritic joint disease hypothyroidism primary cutaneous T-cell lymphoma autoimmune lymphoproliferative syndrome invasive ductal breast carcinoma psoriasis bipolar disorder schizophrenia skin basal cell carcinoma breast disease type 1 diabetes mellitus celiac disease, susceptibility to, 3 lung disease colonic disease lymphatic system disease demyelinating disease malignant colon neoplasm ovarian cancer hematologic disease atopic eczema inborn carbohydrate metabolic disorder renal cell carcinoma brain disease skin disease cancer liver disease chronic obstructive pulmonary disease lupus erythematosus

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.