1D4T | pdb_00001d4t

CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH A SLAM PEPTIDE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	d1d4ta_	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	The Xlp protein Sap	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SH2 domain	8023337	4001650	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SH2 domain	8035717	3000197	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SH2	e1d4tA1	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00017	SH2 domain (SH2)	SH2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE	protein binding binding virus receptor activity exogenous protein binding molecular transducer activity signaling receptor activity SH2 domain binding protein domain specific binding antigen binding identical protein binding transmembrane signaling receptor activity	multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation tumor necrosis factor superfamily cytokine production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity response to stimulus T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of immune response T-helper 1 cell cytokine production leukocyte mediated immunity regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production positive regulation of immune system process regulation of T cell mediated immunity regulation of cytokine production involved in immune response immune response regulation of adaptive immune response T-helper 1 type immune response regulation of T-helper 1 type immune response immune effector process regulation of leukocyte mediated immunity regulation of response to stimulus positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process regulation of immune response regulation of production of molecular mediator of immune response positive regulation of cytokine production positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of T-helper 1 cell cytokine production positive regulation of biological process regulation of T-helper 1 cell cytokine production positive regulation of response to stimulus regulation of T cell cytokine production CD4-positive, alpha-beta T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process positive regulation of immune effector process cytokine production involved in immune response positive regulation of cellular process production of molecular mediator of immune response positive regulation of T-helper 1 type immune response adaptive immune response regulation of lymphocyte mediated immunity positive regulation of gene expression immune system process positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response regulation of localization regulation of cellular component organization transport membrane fusion organelle membrane fusion regulation of vesicle fusion vesicle-mediated transport vesicle organization cellular component organization localization cellular component organization or biogenesis membrane organization regulation of transport regulation of vesicle-mediated transport establishment of localization regulation of organelle organization organelle fusion organelle organization vesicle fusion cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling positive regulation of dendritic cell chemotaxis positive regulation of locomotion regulation of cell motility regulation of response to external stimulus dendritic cell chemotaxis positive regulation of chemotaxis positive regulation of cell migration positive regulation of response to external stimulus taxis positive regulation of cell motility regulation of cell migration positive regulation of mononuclear cell migration cell migration cell motility regulation of mononuclear cell migration locomotion cell chemotaxis chemotaxis regulation of dendritic cell chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration response to external stimulus positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis regulation of chemotaxis leukocyte migration dendritic cell migration cellular response to chemical stimulus response to chemical regulation of locomotion mononuclear cell migration leukocyte chemotaxis interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production import into cell phagocytosis endocytosis biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus macrophage migration positive regulation of macrophage migration granulocyte migration macrophage chemotaxis regulation of granulocyte chemotaxis regulation of macrophage migration myeloid leukocyte migration regulation of macrophage chemotaxis granulocyte chemotaxis positive regulation of macrophage chemotaxis cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of JNK cascade JNK cascade regulation of JNK cascade regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of activated T cell proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation regulation of activated T cell proliferation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation activated T cell proliferation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation natural killer cell activation natural killer cell proliferation negative regulation of signaling negative regulation of cell communication CD40 signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of CD40 signaling pathway negative regulation of signal transduction regulation of CD40 signaling pathway leukocyte chemotaxis involved in inflammatory response leukocyte migration involved in inflammatory response inflammatory response negative regulation of lymphocyte mediated immunity negative regulation of cytokine production involved in immune response negative regulation of immune response negative regulation of immune effector process negative regulation of adaptive immune response negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains negative regulation of production of molecular mediator of immune response negative regulation of T cell mediated immunity negative regulation of T cell cytokine production negative regulation of immune system process negative regulation of leukocyte mediated immunity regulation of type II interferon production type II interferon production negative regulation of type II interferon production regulation of interleukin-12 production negative regulation of interleukin-12 production interleukin-12 production developmental process cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation cell differentiation anatomical structure development natural killer cell differentiation leukocyte differentiation myeloid dendritic cell activation myeloid dendritic cell activation involved in immune response cell activation involved in immune response myeloid leukocyte activation myeloid cell activation involved in immune response leukocyte activation involved in immune response positive regulation of type II interferon production	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 anatomical structure intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle cytoplasm endocytic vesicle
A	T CELL SIGNAL TRANSDUCTION MOLECULE SAP	protein-macromolecule adaptor activity molecular adaptor activity	lymphocyte mediated immunity biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus leukocyte mediated cytotoxicity response to biotic stimulus immune effector process immune system process defense response to other organism response to stress natural killer cell mediated cytotoxicity lymphocyte mediated immunity biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus leukocyte mediated cytotoxicity response to biotic stimulus immune effector process immune system process defense response to other organism response to stress natural killer cell mediated cytotoxicity innate immune response leukocyte mediated immunity cellular process response to external biotic stimulus natural killer cell mediated immunity cell killing regulation of immune effector process positive regulation of leukocyte mediated immunity positive regulation of response to biotic stimulus regulation of cellular process positive regulation of leukocyte mediated cytotoxicity positive regulation of immune response positive regulation of natural killer cell mediated immunity regulation of immune system process positive regulation of immune system process regulation of biological process regulation of natural killer cell mediated immunity regulation of innate immune response regulation of leukocyte mediated immunity regulation of response to stimulus positive regulation of defense response regulation of immune response positive regulation of natural killer cell mediated cytotoxicity regulation of cell killing positive regulation of cell killing regulation of defense response regulation of response to biotic stimulus regulation of natural killer cell mediated cytotoxicity regulation of response to external stimulus positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus regulation of response to stress positive regulation of immune effector process positive regulation of cellular process positive regulation of innate immune response regulation of leukocyte mediated cytotoxicity biological regulation regulation of lymphocyte mediated immunity cellular response to stimulus immune response-regulating cell surface receptor signaling pathway signaling negative regulation of signaling negative regulation of biological process regulation of signal transduction regulation of antigen receptor-mediated signaling pathway negative regulation of antigen receptor-mediated signaling pathway negative regulation of cell communication cell communication immune response-activating signaling pathway immune response-regulating signaling pathway negative regulation of cellular process signal transduction regulation of signaling cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway negative regulation of response to stimulus regulation of T cell receptor signaling pathway T cell receptor signaling pathway negative regulation of signal transduction negative regulation of T cell receptor signaling pathway negative regulation of immune system process regulation of cell communication antigen receptor-mediated signaling pathway activation of immune response adaptive immune response multicellular organismal process cell activation natural killer cell activation lymphocyte activation leukocyte activation humoral immune response cellular defense response cell-cell signaling	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR010407	Signaling lymphocytic activation molecule, N-terminal	Domain
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR015631	CD2/SLAM family receptor	Family
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR007110	Immunoglobulin-like domain	Domain
A	IPR036860	SH2 domain superfamily	Homologous Superfamily
A	IPR000980	SH2 domain	Domain
A	IPR035876	SH2D1A, SH2 domain	Domain
A	IPR017289	SH2 protein 1A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q13291	atopic eczema Malignant neoplasm of breast psoriasis cutaneous lupus erythematosus measles Sjogren syndrome interstitial cystitis osteosarcoma ulcerative colitis
A	Pharos: O60880	lymphoproliferative syndrome X-linked lymphoproliferative disease due to SH2D1A deficiency chronic obstructive pulmonary disease head and neck cancer interstitial cystitis sarcoidosis cutaneous lupus erythematosus hematopoietic and lymphoid system neoplasm lung cancer osteosarcoma Sjogren syndrome X-linked lymphoproliferative syndrome dysgammaglobulinemia hemophagocytic syndrome Lymphoproliferative Disorders lymphoproliferative syndrome X-linked lymphoproliferative disease due to SH2D1A deficiency chronic obstructive pulmonary disease head and neck cancer interstitial cystitis sarcoidosis cutaneous lupus erythematosus hematopoietic and lymphoid system neoplasm lung cancer osteosarcoma Sjogren syndrome X-linked lymphoproliferative syndrome dysgammaglobulinemia hemophagocytic syndrome Lymphoproliferative Disorders psoriasis ulcerative colitis

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.