3DZF | pdb_00003dzf

Crystal structure of human CD38 extracellular domain complexed with a covalent intermediate, ara-F-ribose-5'-phosphate

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)
F	d3dzff_	Alpha and beta proteins (a/b)	Flavodoxin-like	N-(deoxy)ribosyltransferase-like	ADP ribosyl cyclase-like	ADP ribosyl cyclase	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3dzfe_	Alpha and beta proteins (a/b)	Flavodoxin-like	N-(deoxy)ribosyltransferase-like	ADP ribosyl cyclase-like	ADP ribosyl cyclase	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3dzfd_	Alpha and beta proteins (a/b)	Flavodoxin-like	N-(deoxy)ribosyltransferase-like	ADP ribosyl cyclase-like	ADP ribosyl cyclase	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3dzfc_	Alpha and beta proteins (a/b)	Flavodoxin-like	N-(deoxy)ribosyltransferase-like	ADP ribosyl cyclase-like	ADP ribosyl cyclase	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3dzfb_	Alpha and beta proteins (a/b)	Flavodoxin-like	N-(deoxy)ribosyltransferase-like	ADP ribosyl cyclase-like	ADP ribosyl cyclase	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3dzfa_	Alpha and beta proteins (a/b)	Flavodoxin-like	N-(deoxy)ribosyltransferase-like	ADP ribosyl cyclase-like	ADP ribosyl cyclase	(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)
F	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8033922	3001392	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8033922	3001392	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8033922	3001392	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8033922	3001392	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8033922	3001392	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	N-(deoxy)ribosyltransferase-like	8033922	3001392	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)
F	Rib_hydrolayse	e3dzfF1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: N-deoxyribosyltransferase (From Topology)	T: N-deoxyribosyltransferase	F: Rib_hydrolayse	ECOD (1.6)
E	Rib_hydrolayse	e3dzfE1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: N-deoxyribosyltransferase (From Topology)	T: N-deoxyribosyltransferase	F: Rib_hydrolayse	ECOD (1.6)
D	Rib_hydrolayse	e3dzfD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: N-deoxyribosyltransferase (From Topology)	T: N-deoxyribosyltransferase	F: Rib_hydrolayse	ECOD (1.6)
C	Rib_hydrolayse	e3dzfC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: N-deoxyribosyltransferase (From Topology)	T: N-deoxyribosyltransferase	F: Rib_hydrolayse	ECOD (1.6)
B	Rib_hydrolayse	e3dzfB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: N-deoxyribosyltransferase (From Topology)	T: N-deoxyribosyltransferase	F: Rib_hydrolayse	ECOD (1.6)
A	Rib_hydrolayse	e3dzfA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: N-deoxyribosyltransferase (From Topology)	T: N-deoxyribosyltransferase	F: Rib_hydrolayse	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.20.82.10	Mainly Alpha	Up-down Bundle	ADP Ribosyl Cyclase	Chain A, domain 1	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	1.20.82.10	Mainly Alpha	Up-down Bundle	ADP Ribosyl Cyclase	Chain A, domain 1	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	1.20.82.10	Mainly Alpha	Up-down Bundle	ADP Ribosyl Cyclase	Chain A, domain 1	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	1.20.82.10	Mainly Alpha	Up-down Bundle	ADP Ribosyl Cyclase	Chain A, domain 1	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.20.82.10	Mainly Alpha	Up-down Bundle	ADP Ribosyl Cyclase	Chain A, domain 1	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	1.20.82.10	Mainly Alpha	Up-down Bundle	ADP Ribosyl Cyclase	Chain A, domain 1	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02267	ADP-ribosyl cyclase (Rib_hydrolayse)	ADP-ribosyl cyclase	ADP-ribosyl cyclase EC:3.2.2.5 (also know as cyclic ADP-ribose hydrolase or CD38) synthesises cyclic-ADP ribose, a second messenger for glucose-induced insulin secretion.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	ADP-ribosyl cyclase 1	hydrolase activity, acting on glycosyl bonds NAD+ nucleosidase activity, cyclic ADP-ribose generating hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity phosphorus-oxygen lyase activity lyase activity transferase activity identical protein binding protein binding binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to stimulus response to chemical response to xenobiotic stimulus regulation of growth regulation of cellular component organization growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular component organization or biogenesis positive regulation of cellular process positive regulation of cytosolic calcium ion concentration regulation of biological quality cellular response to stimulus immune response-regulating cell surface receptor signaling pathway signaling cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response regulation of tube diameter multicellular organismal process system process regulation of tube size regulation of system process positive regulation of vasoconstriction circulatory system process regulation of blood circulation vascular process in circulatory system regulation of vasoconstriction positive regulation of multicellular organismal process regulation of multicellular organismal process blood vessel diameter maintenance vasoconstriction blood circulation regulation of anatomical structure size multi-multicellular organism process reproductive process female pregnancy multi-organism reproductive process response to ketone response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to progesterone response to oxygen-containing compound negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death response to peptide response to cytokine response to interleukin-1 nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process nucleotide metabolic process purine-containing compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process NAD+ metabolic process response to retinoic acid regulation of neuron projection development cellular developmental process cell projection organization cell development neuron projection development neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation mononuclear cell proliferation lymphocyte proliferation negative regulation of tissue remodeling homeostatic process negative regulation of bone remodeling regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption negative regulation of bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis negative regulation of multicellular organismal process response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus vascular associated smooth muscle contraction muscle contraction muscle system process smooth muscle contraction artery smooth muscle contraction tonic smooth muscle contraction positive regulation of DNA-templated transcription 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 RNA metabolic process positive regulation of RNA biosynthetic process apoptotic signaling pathway response to oxidative stress response to hydroperoxide negative regulation of signaling modulation of chemical synaptic transmission negative regulation of synaptic transmission negative regulation of cell communication synaptic signaling regulation of synaptic plasticity trans-synaptic signaling regulation of signaling cell-cell signaling chemical synaptic transmission regulation of trans-synaptic signaling long-term synaptic depression anterograde trans-synaptic signaling regulation of cell communication positive regulation of cell population proliferation positive regulation of B cell proliferation regulation of leukocyte activation regulation of cell activation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation positive regulation of B cell activation regulation of cell population proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization localization positive regulation of insulin secretion intracellular protein localization regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion establishment of localization regulation of protein secretion regulation of secretion positive regulation of protein localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion regulation of transport secretion regulation of peptide transport regulation of establishment of protein localization export from cell regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion positive regulation of signaling response to estradiol	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane extracellular exosome cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cell surface cell periphery plasma membrane basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR003193	ADP-ribosyl cyclase (CD38/157)	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P28907	Liver Cirrhosis, Experimental psoriasis ulcerative colitis acquired metabolic disease B-cell chronic lymphocytic leukemia coronary artery disease Duchenne muscular dystrophy lymphatic system disease periodontitis Sjogren syndrome bone marrow disease cutaneous lupus erythematosus HIV infectious disease lung cancer myocardial ischemia Liver Cirrhosis, Experimental psoriasis ulcerative colitis acquired metabolic disease B-cell chronic lymphocytic leukemia coronary artery disease Duchenne muscular dystrophy lymphatic system disease periodontitis Sjogren syndrome bone marrow disease cutaneous lupus erythematosus HIV infectious disease lung cancer myocardial ischemia plasma cell myeloma astrocytic tumor cancer diabetes mellitus interstitial cystitis lung carcinoma osteosarcoma

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.