6A3W

Complex structure of 4-1BB and utomilumab

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)
D	d6a3wd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6a3wg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6a3wa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d6a3wj_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6a3wb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6a3we_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6a3wh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d6a3wk_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	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)
C	TNFR_c6	e6a3wC2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
C	TNFRSF5	e6a3wC3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF5	ECOD (1.6)
C	TNFRSF14	e6a3wC1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF14	ECOD (1.6)
I	TNFR_c6	e6a3wI3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
I	TNFRSF5	e6a3wI2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF5	ECOD (1.6)
I	TNFRSF14	e6a3wI1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF14	ECOD (1.6)
F	TNFRSF14	e6a3wF1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF14	ECOD (1.6)
F	UNK_F_TYPE	e6a3wF2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: UNK_F_TYPE	ECOD (1.6)
L	TNFR_c6	e6a3wL1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
L	TNFRSF14	e6a3wL2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF14	ECOD (1.6)
L	UNK_F_TYPE	e6a3wL3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: UNK_F_TYPE	ECOD (1.6)
D	V-set_8	e6a3wD1	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)
G	V-set_8	e6a3wG1	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	V-set_8	e6a3wA1	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)
J	V-set_8	e6a3wJ1	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)
B	V-set_3	e6a3wB1	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	V-set_3	e6a3wE1	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)
H	V-set_3	e6a3wH1	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)
K	V-set_3	e6a3wK1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (utative)
I	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, D, G, J	mAb utomilumab	VH	Homo sapiens (human)	IGHV5-10-104, IGHJ401, IGHJ402, IGHJ403	V-DOMAIN VH	IG	FV-HEAVY_LAMBDA	IMGT (202443-0)
B, E, H, K	mAb utomilumab	V-LAMBDA	Homo sapiens (human)	IGLV3-101, IGLJ201, IGLJ302, IGLJ101, IGLJ3*01	V-DOMAIN V-LAMBDA	IG	FV-HEAVY_LAMBDA	IMGT (202443-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D, G, J	Heavy Chain	IGHV5	-	tumor necrosis factor receptor superfamily member 9	SAbDab (2024-11-01)
B, E, H, K	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, D, G, J	Utomilumab	TNFRSF9/CD137/4-1BB	Therapeutic SAbDab (2024-11-01)
B, E, H, K	Utomilumab	TNFRSF9/CD137/4-1BB	Therapeutic SAbDab (2024-11-01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I, L	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
C, F, I, L	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
A, D, G, J	utomilumab VH	-	-	-
B, E, H, K	utomilumab VL	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F, I, L	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.