3D0Y | pdb_00003d0y

Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3d0yb_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	Calcyclin (S100)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3d0ya_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	Calcyclin (S100)	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)
B	SCOP2B Superfamily	EF-hand	8042162	3001983	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-hand	8042162	3001983	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)
B		e3d0yB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Methyltransf_25	F:	ECOD (20:10:01)
A		e3d0yA1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Methyltransf_25	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
A	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF01023	S-100/ICaBP type calcium binding domain (S_100)	S-100/ICaBP type calcium binding domain	The S-100 domain is a subfamily of the EF-hand calcium binding proteins.	Domain
B	PF00036	EF hand domain (EF-hand_1)	EF hand domain	The EF-hands can be divided into two classes: signalling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typica ...	The EF-hands can be divided into two classes: signalling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site. The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes.	Domain
A	PF01023	S-100/ICaBP type calcium binding domain (S_100)	S-100/ICaBP type calcium binding domain	The S-100 domain is a subfamily of the EF-hand calcium binding proteins.	Domain
A	PF00036	EF hand domain (EF-hand_1)	EF hand domain	The EF-hands can be divided into two classes: signalling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typica ...	The EF-hands can be divided into two classes: signalling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site. The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Protein S100-B	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding S100 protein binding identical protein binding protein homodimerization activity protein dimerization activity cytoskeletal protein binding tau protein binding RAGE receptor binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding S100 protein binding identical protein binding protein homodimerization activity protein dimerization activity cytoskeletal protein binding tau protein binding RAGE receptor binding signaling receptor binding calcium-dependent protein binding transition metal ion binding zinc ion binding	multicellular organismal process multicellular organismal-level homeostasis homeostatic process temperature homeostasis adaptive thermogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction multicellular organismal process multicellular organismal-level homeostasis homeostatic process temperature homeostasis adaptive thermogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB 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 regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling developmental process multicellular organism development central nervous system development anatomical structure development nervous system development system development response to chemical response to methylmercury response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death behavior system process learning or memory nervous system process cognition memory cellular developmental process developmental growth cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell growth cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis neuron projection extension plasma membrane bounded cell projection organization developmental cell growth growth sympathetic neuron projection extension developmental growth involved in morphogenesis generation of neurons anatomical structure morphogenesis neuron development skeletal muscle cell differentiation regulation of developmental process skeletal muscle tissue development negative regulation of biological process regulation of cell differentiation striated muscle tissue development muscle structure development skeletal muscle organ development regulation of skeletal muscle cell differentiation negative regulation of cellular process negative regulation of skeletal muscle cell differentiation negative regulation of cell differentiation muscle tissue development muscle organ development negative regulation of developmental process animal organ development tissue development response to anesthetic response to corticosteroid response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to glucocorticoid axonogenesis axon development cell morphogenesis involved in neuron differentiation response to alcohol response to oxygen-containing compound response to ethanol regulation of cell shape regulation of cell morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation regulation of myelination regulation of system process regulation of nervous system development positive regulation of myelination axon ensheathment ensheathment of neurons positive regulation of nervous system process regulation of multicellular organismal process regulation of multicellular organismal development regulation of nervous system process myelination positive regulation of multicellular organismal process astrocyte differentiation gliogenesis glial cell differentiation regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling positive regulation of neuron differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of neuron differentiation cell adhesion long-term synaptic potentiation positive regulation of synaptic transmission	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton extracellular region ruffle cell leading edge perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body extracellular space ciliary basal body microtubule organizing center
A	Protein S100-B	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding S100 protein binding identical protein binding protein homodimerization activity protein dimerization activity cytoskeletal protein binding tau protein binding RAGE receptor binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding S100 protein binding identical protein binding protein homodimerization activity protein dimerization activity cytoskeletal protein binding tau protein binding RAGE receptor binding signaling receptor binding calcium-dependent protein binding transition metal ion binding zinc ion binding	multicellular organismal process multicellular organismal-level homeostasis homeostatic process temperature homeostasis adaptive thermogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction multicellular organismal process multicellular organismal-level homeostasis homeostatic process temperature homeostasis adaptive thermogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB 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 regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling developmental process multicellular organism development central nervous system development anatomical structure development nervous system development system development response to chemical response to methylmercury response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death behavior system process learning or memory nervous system process cognition memory cellular developmental process developmental growth cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell growth cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis neuron projection extension plasma membrane bounded cell projection organization developmental cell growth growth sympathetic neuron projection extension developmental growth involved in morphogenesis generation of neurons anatomical structure morphogenesis neuron development skeletal muscle cell differentiation regulation of developmental process skeletal muscle tissue development negative regulation of biological process regulation of cell differentiation striated muscle tissue development muscle structure development skeletal muscle organ development regulation of skeletal muscle cell differentiation negative regulation of cellular process negative regulation of skeletal muscle cell differentiation negative regulation of cell differentiation muscle tissue development muscle organ development negative regulation of developmental process animal organ development tissue development response to anesthetic response to corticosteroid response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to glucocorticoid axonogenesis axon development cell morphogenesis involved in neuron differentiation response to alcohol response to oxygen-containing compound response to ethanol regulation of cell shape regulation of cell morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation regulation of myelination regulation of system process regulation of nervous system development positive regulation of myelination axon ensheathment ensheathment of neurons positive regulation of nervous system process regulation of multicellular organismal process regulation of multicellular organismal development regulation of nervous system process myelination positive regulation of multicellular organismal process astrocyte differentiation gliogenesis glial cell differentiation regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling positive regulation of neuron differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of neuron differentiation cell adhesion long-term synaptic potentiation positive regulation of synaptic transmission	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton extracellular region ruffle cell leading edge perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body extracellular space ciliary basal body microtubule organizing center

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR001751	S100/Calcium binding protein 7/8-like, conserved site	Conserved Site
B	IPR002048	EF-hand domain	Domain
B	IPR011992	EF-hand domain pair	Homologous Superfamily
B	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
B	IPR028481	Protein S100-B	Family
B	IPR013787	S100/CaBP-9k-type, calcium binding, subdomain	Domain
A	IPR001751	S100/Calcium binding protein 7/8-like, conserved site	Conserved Site
A	IPR002048	EF-hand domain	Domain
A	IPR011992	EF-hand domain pair	Homologous Superfamily
A	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
A	IPR028481	Protein S100-B	Family
A	IPR013787	S100/CaBP-9k-type, calcium binding, subdomain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P04271	Down syndrome Hematoma bipolar disorder myocardial infarction oppositional defiant disorder intracranial vasospasm brain edema interstitial cystitis invasive ductal breast carcinoma malignant colon neoplasm brain injury neurodegenerative disease cerebrovascular disorder psoriasis ductal breast carcinoma in situ Down syndrome Hematoma bipolar disorder myocardial infarction oppositional defiant disorder intracranial vasospasm brain edema interstitial cystitis invasive ductal breast carcinoma malignant colon neoplasm brain injury neurodegenerative disease cerebrovascular disorder psoriasis ductal breast carcinoma in situ human African trypanosomiasis intracerebral hemorrhage atypical teratoid rhabdoid tumor large cell medulloblastoma brain cancer medulloblastoma breast cancer pneumocystosis depressive disorder schizophrenia fetal methylmercury syndrome major depressive disorder breast carcinoma pituitary cancer
A	Pharos: P04271	Down syndrome Hematoma bipolar disorder myocardial infarction oppositional defiant disorder intracranial vasospasm brain edema interstitial cystitis invasive ductal breast carcinoma malignant colon neoplasm brain injury neurodegenerative disease cerebrovascular disorder psoriasis ductal breast carcinoma in situ Down syndrome Hematoma bipolar disorder myocardial infarction oppositional defiant disorder intracranial vasospasm brain edema interstitial cystitis invasive ductal breast carcinoma malignant colon neoplasm brain injury neurodegenerative disease cerebrovascular disorder psoriasis ductal breast carcinoma in situ human African trypanosomiasis intracerebral hemorrhage atypical teratoid rhabdoid tumor large cell medulloblastoma brain cancer medulloblastoma breast cancer pneumocystosis depressive disorder schizophrenia fetal methylmercury syndrome major depressive disorder breast carcinoma pituitary cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	FME	Parent Component: MET RESID: AA0021 , AA0566 PSI-MOD : N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.