6MI2

Structure of the human 4-1BB / Utomilumab Fab complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-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)
B	d6mi2b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6mi2b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth E]	d6mi2e2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth E]	d6mi2e1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	V-set_8	e6mi2A2	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)
A	C1-set_1	e6mi2A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth D]	V-set_8	e6mi2D1	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)
C [auth D]	C1-set_1	e6mi2D2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B	C1-set	e6mi2B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
B	V-set_3	e6mi2B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D [auth E]	C1-set	e6mi2E2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
D [auth E]	V-set_3	e6mi2E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
E [auth F]	TNFR_c6	e6mi2F2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
E [auth F]	TNFRSF5	e6mi2F3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF5	ECOD (1.6)
E [auth F]	TNFRSF14	e6mi2F1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF14	ECOD (1.6)
F [auth C]	TNFR_c6	e6mi2C1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
F [auth C]	TNFRSF5	e6mi2C2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF5	ECOD (1.6)
F [auth C]	TNFRSF14	e6mi2C3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF14	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 (utative)
C [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth F]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (utative)
F [auth C]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (utative)

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, C [auth D]	Fab Urelumab	VH-CH1	Homo sapiens (human)	IGHV5-10-104, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202443-0)
B, D [auth E]	Fab Urelumab	L-LAMBDA	Homo sapiens (human)	IGLV3-101, IGLJ201, IGLJ302, IGLJ101, IGLJ301, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202443-0)
E [auth F], F [auth C]	TNFRSF9 (Tumor necrosis factor receptor superfamily member 9)	1C-LIKE	Homo sapiens (human)	TNFRSF9*01	M-LIKE-DOMAIN TNFR-CYS	RPI	4TNFR-CYS	IMGT (202443-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C [auth D]	Heavy Chain	IGHV5	-	tumor necrosis factor receptor superfamily member 9	SAbDab (2024-11-01)
B, D [auth E]	Light Chain	IGLV3	Lambda	tumor necrosis factor receptor superfamily member 9	SAbDab (2024-11-01)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A, C [auth D]	Utomilumab	TNFRSF9/CD137/4-1BB	Therapeutic SAbDab (2024-11-01)
B, D [auth E]	Utomilumab	TNFRSF9/CD137/4-1BB	Therapeutic SAbDab (2024-11-01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth F], F [auth C]	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth D]	Utomilumab Fab heavy chain	-	-	-
B, D [auth E]	Utomilumab Fab lambda chain	-	-	-
E [auth F], F [auth C]	Tumor necrosis factor receptor superfamily member 9	molecular transducer activity signaling receptor activity	cellular process apoptotic process cell death programmed cell death negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process multicellular organismal process cellular developmental process cellular process apoptotic process cell death programmed cell death negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process multicellular organismal process cellular developmental process regulation of leukocyte activation immature T cell proliferation in thymus regulation of cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte proliferation leukocyte activation T cell differentiation in thymus T cell activation cell differentiation lymphocyte proliferation anatomical structure development regulation of immature T cell proliferation regulation of multicellular organismal process regulation of immune system process T cell differentiation T cell proliferation regulation of lymphocyte proliferation developmental process regulation of leukocyte proliferation hemopoiesis cell activation regulation of T cell activation immature T cell proliferation regulation of immature T cell proliferation in thymus regulation of T cell proliferation mononuclear cell proliferation immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation leukocyte differentiation	cell periphery plasma membrane membrane cellular anatomical entity cell surface external side of plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth F], F [auth C]	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
E [auth F], F [auth C]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
E [auth F], F [auth C]	IPR020413	Tumour necrosis factor receptor 9	Family
E [auth F], F [auth C]	IPR034020	Tumour necrosis factor receptor 9, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth F], F [auth C]	Pharos: Q07011	ulcerative colitis malignant colon neoplasm medulloblastoma tuberculosis benign colon neoplasm colorectal cancer gastric cancer hereditary diffuse gastric adenocarcinoma kidney cancer lung cancer Malignant neoplasm of kidney psoriasis cancer Crohn disease gastric neoplasm ulcerative colitis malignant colon neoplasm medulloblastoma tuberculosis benign colon neoplasm colorectal cancer gastric cancer hereditary diffuse gastric adenocarcinoma kidney cancer lung cancer Malignant neoplasm of kidney psoriasis cancer Crohn disease gastric neoplasm inflammatory bowel disease kidney neoplasm lymphatic system disease rheumatoid arthritis colonic neoplasm cutaneous lupus erythematosus hematologic disease interstitial cystitis lung adenocarcinoma

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.