8DS5 | pdb_00008ds5

X-ray structure of the MK5890 Fab - CD27 antibody-antigen complex

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TNFR_c6_2	e8ds5A2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_2	ECOD (1.6)
A	TNFR_c6_1	e8ds5A1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_1	ECOD (1.6)
B	C1-set_4	e8ds5B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e8ds5B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C	V-set_8	e8ds5C2	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	C1-set_1	e8ds5C1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Light Chain	IGKV3	Kappa	cd27 antigen	SAbDab (2025-09-26)
C	Heavy Chain	IGHV9	-	cd27 antigen	SAbDab (2025-09-26)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B	Boserolimab	TNFRSF7/CD27	Therapeutic SAbDab (2025-09-26)
C	Boserolimab	TNFRSF7/CD27	Therapeutic SAbDab (2025-09-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	CD27 antigen	enzyme regulator activity cysteine-type endopeptidase inhibitor activity involved in apoptotic process molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade biological regulation regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity immune response B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process adaptive immune memory response adaptive immune memory response involving T cells and B cells immunological memory process cell surface receptor signaling pathway CD27 signaling pathway negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process leukocyte apoptotic process negative regulation of T cell apoptotic process lymphocyte apoptotic process negative regulation of leukocyte apoptotic process regulation of T cell apoptotic process T cell apoptotic process negative regulation of lymphocyte apoptotic process extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation regulation of cell differentiation positive regulation of B cell differentiation lymphocyte differentiation regulation of cell development positive regulation of developmental process positive regulation of cell activation multicellular organism development cell differentiation positive regulation of leukocyte activation anatomical structure development regulation of immune system process positive regulation of immune system process developmental process positive regulation of cell development positive regulation of multicellular organismal process leukocyte differentiation cellular developmental process regulation of developmental process cell development positive regulation of lymphocyte activation regulation of B cell differentiation B cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of B cell activation regulation of multicellular organismal process regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis B cell activation positive regulation of B cell activation regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation positive regulation of T cell differentiation T cell differentiation positive regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of T cell differentiation cell adhesion cell-cell adhesion regulation of cell-cell adhesion positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation response to alcohol response to chemical response to oxygen-containing compound response to ethanol	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular region
B	MK-5890 Fab light chain	-	-	-
C	MK-5890 Fab heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR022328	Tumour necrosis factor receptor 7	Family
A	IPR034000	Tumour necrosis factor receptor 7, N-terminal	Domain
A	IPR001368	TNFR/NGFR cysteine-rich region	Domain
A	IPR053126	CD27 antigen receptor	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P26842	lymphoproliferative syndrome 2 Cachexia plasma cell myeloma agammaglobulinemia Crohn disease interstitial cystitis lymphatic system disease non-small cell lung carcinoma peripheral nervous system disease psoriasis autoimmune disease cancer cutaneous lupus erythematosus juvenile idiopathic arthritis osteosarcoma lymphoproliferative syndrome 2 Cachexia plasma cell myeloma agammaglobulinemia Crohn disease interstitial cystitis lymphatic system disease non-small cell lung carcinoma peripheral nervous system disease psoriasis autoimmune disease cancer cutaneous lupus erythematosus juvenile idiopathic arthritis osteosarcoma peripheral neuropathy ulcerative colitis B-cell chronic lymphocytic leukemia celiac disease hematologic disease lung adenocarcinoma periodontitis

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.