7XAD | pdb_00007xad

Crystal strucutre of PD-L1 and DBL2_02 designed protein binder

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
H [auth I]	SCOP2B Superfamily	t-snare proteins	8067986	3000366	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	t-snare proteins	8067986	3000366	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	t-snare proteins	8067986	3000366	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	t-snare proteins	8067986	3000366	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)
H [auth I]	F_UNCLASSIFIED	e7xadI1	A: alpha bundles	X: STAT-like	H: t-snare proteins (From Topology)	T: t-snare proteins	F: F_UNCLASSIFIED	ECOD (1.6)
F [auth G]	F_UNCLASSIFIED	e7xadG1	A: alpha bundles	X: STAT-like	H: t-snare proteins (From Topology)	T: t-snare proteins	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth E]	F_UNCLASSIFIED	e7xadE1	A: alpha bundles	X: STAT-like	H: t-snare proteins (From Topology)	T: t-snare proteins	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth C]	F_UNCLASSIFIED	e7xadC1	A: alpha bundles	X: STAT-like	H: t-snare proteins (From Topology)	T: t-snare proteins	F: F_UNCLASSIFIED	ECOD (1.6)
G [auth H]	F_UNCLASSIFIED	e7xadH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
E [auth F]	F_UNCLASSIFIED	e7xadF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth D]	F_UNCLASSIFIED	e7xadD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e7xadA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], D [auth E], F [auth G], H [auth I]	PF05008	Vesicle transport v-SNARE protein N-terminus (V-SNARE)	Vesicle transport v-SNARE protein N-terminus	V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this [1]. This domain is the N-terminal half of the V-Snare proteins ...	V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this [1]. This domain is the N-terminal half of the V-Snare proteins.	Domain
A, C [auth D], E [auth F], G [auth H]	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
A, C [auth D], E [auth F], G [auth H]	PF08205	CD80-like C2-set immunoglobulin domain (C2-set_2)	CD80-like C2-set immunoglobulin domain	These domains belong to the immunoglobulin superfamily.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D [auth E], F [auth G], H [auth I]	DBL2_02 binder	SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding SNARE binding	inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis vacuolar calcium ion homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cellular localization post-Golgi vesicle-mediated transport inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis vacuolar calcium ion homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cellular localization post-Golgi vesicle-mediated transport transport intracellular transport establishment of localization vesicle-mediated transport Golgi to vacuole transport localization establishment of localization in cell vacuolar transport cellular process Golgi vesicle transport import into cell endocytosis membrane organization membrane fusion organelle membrane fusion vesicle organization cellular component organization organelle fusion organelle organization cellular component organization or biogenesis vesicle fusion Golgi vesicle fusion to target membrane vacuole fusion vacuole organization vacuole fusion, non-autophagic catabolic process macroautophagy autophagy amphisome-lysosome fusion metabolic process process utilizing autophagic mechanism intra-Golgi vesicle-mediated transport establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization intracellular protein transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi vesicle fusion with Golgi apparatus Golgi organization endomembrane system organization Golgi to endosome transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol SNARE complex protein-containing complex membrane membrane protein complex membrane-bounded organelle endosome membrane endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol SNARE complex protein-containing complex membrane membrane protein complex membrane-bounded organelle endosome membrane endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle late endosome vesicle organelle membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane storage vacuole lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane fungal-type vacuole membrane autophagosome membrane autophagosome Golgi apparatus Golgi membrane transport vesicle transport vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane coated vesicle
A, C [auth D], E [auth F], G [auth H]	Programmed cell death 1 ligand 1	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process leukocyte apoptotic process positive regulation of biological process regulation of programmed cell death lymphocyte apoptotic process regulation of activated CD8-positive, alpha-beta T cell apoptotic process activated CD8-positive, alpha-beta T cell apoptotic process regulation of T cell apoptotic process positive regulation of leukocyte apoptotic process positive regulation of cellular process regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process regulation of biological process positive regulation of programmed cell death regulation of cellular process leukocyte apoptotic process positive regulation of biological process regulation of programmed cell death lymphocyte apoptotic process regulation of activated CD8-positive, alpha-beta T cell apoptotic process activated CD8-positive, alpha-beta T cell apoptotic process regulation of T cell apoptotic process positive regulation of leukocyte apoptotic process positive regulation of cellular process regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process regulation of biological process positive regulation of programmed cell death positive regulation of lymphocyte apoptotic process regulation of apoptotic process biological regulation cell death positive regulation of apoptotic process positive regulation of T cell apoptotic process positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process cellular process T cell apoptotic process apoptotic process programmed cell death negative regulation of lymphocyte proliferation multicellular organismal process regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of immune system process regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of activated T cell proliferation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation activated T cell proliferation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of activated T cell proliferation negative regulation of immune system process immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation response to stimulus immune response adaptive immune response cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus pattern recognition receptor signaling pathway regulation of response to external stimulus toll-like receptor signaling pathway signaling cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of innate immune response defense response regulation of innate immune response defense response to symbiont TRIF-dependent toll-like receptor signaling pathway regulation of response to stimulus defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response MyD88-independent toll-like receptor signaling pathway activation of immune response response to peptide response to cytokine negative regulation of interleukin-10 production interleukin-10 production regulation of cytokine production cytokine production regulation of interleukin-10 production negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cell surface receptor signaling pathway tumor necrosis factor superfamily cytokine production regulation of tumor necrosis factor superfamily cytokine production negative regulation of tumor necrosis factor superfamily cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of interleukin-10 production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production regulation of type II interferon production type II interferon production negative regulation of type II interferon production adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity negative regulation of response to biotic stimulus immune response to tumor cell negative regulation of immune response to tumor cell negative regulation of response to tumor cell negative regulation of lymphocyte mediated immunity regulation of response to tumor cell T cell mediated immune response to tumor cell negative regulation of T cell mediated immune response to tumor cell regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of T cell mediated immune response to tumor cell leukocyte mediated immunity regulation of T cell mediated immunity response to tumor cell regulation of adaptive immune response negative regulation of response to stimulus negative regulation of immune response negative regulation of immune effector process regulation of immune response to tumor cell negative regulation of adaptive immune response immune effector process negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity negative regulation of leukocyte mediated immunity negative regulation of T cell mediated immunity positive regulation of leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation positive regulation of leukocyte activation positive regulation of T cell activation positive regulation of cell adhesion lymphocyte costimulation T cell costimulation regulation of alpha-beta T cell activation alpha-beta T cell proliferation alpha-beta T cell activation regulation of CD4-positive, alpha-beta T cell proliferation negative regulation of CD4-positive, alpha-beta T cell activation regulation of alpha-beta T cell proliferation CD4-positive, alpha-beta T cell activation CD4-positive, alpha-beta T cell proliferation negative regulation of alpha-beta T cell proliferation regulation of CD4-positive, alpha-beta T cell activation negative regulation of CD4-positive, alpha-beta T cell proliferation negative regulation of alpha-beta T cell activation positive regulation of cell population proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of leukocyte proliferation positive regulation of mononuclear cell proliferation CD8-positive, alpha-beta T cell activation negative regulation of CD8-positive, alpha-beta T cell activation regulation of CD8-positive, alpha-beta T cell activation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoskeleton membraneless organelle intracellular membraneless organelle actin cytoskeleton nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endosome membrane endosome intracellular vesicle recycling endosome endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane cytoplasmic vesicle cytoplasm organelle membrane early endosome early endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D [auth E], F [auth G], H [auth I]	IPR038407	Vesicle transport v-SNARE, N-terminal domain superfamily	Homologous Superfamily
B [auth C], D [auth E], F [auth G], H [auth I]	IPR000727	Target SNARE coiled-coil homology domain	Domain
B [auth C], D [auth E], F [auth G], H [auth I]	IPR027027	GOSR2/Membrin/Bos1	Family
B [auth C], D [auth E], F [auth G], H [auth I]	IPR007705	Vesicle transport v-SNARE, N-terminal	Domain
B [auth C], D [auth E], F [auth G], H [auth I]	IPR010989	SNARE	Homologous Superfamily
A, C [auth D], E [auth F], G [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, C [auth D], E [auth F], G [auth H]	IPR013106	Immunoglobulin V-set domain	Domain
A, C [auth D], E [auth F], G [auth H]	IPR003599	Immunoglobulin domain subtype	Domain
A, C [auth D], E [auth F], G [auth H]	IPR051713	T-cell Activation and Immune Regulation Protein	Family
A, C [auth D], E [auth F], G [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C [auth D], E [auth F], G [auth H]	IPR013162	CD80-like, immunoglobulin C2-set	Domain
A, C [auth D], E [auth F], G [auth H]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth D], E [auth F], G [auth H]	Pharos: Q9NZQ7	thymus cancer lymphoma non-small cell lung carcinoma allergic disease hepatocellular carcinoma cancer Neoplasms, Radiation-Induced pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia drug dependence prostate disease head and neck cancer skin disease interstitial cystitis substance abuse liver disease thymus cancer lymphoma non-small cell lung carcinoma allergic disease hepatocellular carcinoma cancer Neoplasms, Radiation-Induced pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia drug dependence prostate disease head and neck cancer skin disease interstitial cystitis substance abuse liver disease atopic eczema lung disease breast cancer transitional cell carcinoma urinary bladder disease congestive heart failure cystic fibrosis osteosarcoma polycystic ovary syndrome psoriasis hematologic disease renal cell carcinoma small cell lung carcinoma kidney disease lung benign neoplasm substance-related disorder autoimmune disease thymus neoplasm breast disease tuberculosis chronic obstructive pulmonary disease nasopharyngeal carcinoma uterine disease connective tissue disease oligodendroglioma diffuse large B-cell lymphoma ovarian disease Hashimoto thyroiditis sarcoidosis hypothyroidism stomach disease substance dependence asthma lung carcinoma brain disease lymphatic system disease trabecular adenocarcinoma medulloblastoma ulcerative colitis colonic disease Crohn disease

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.