2H61

X-ray structure of human Ca2+-loaded S100B

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	d2h61b_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2h61f_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2h61h_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2h61a_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2h61e_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2h61c_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2h61d_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d2h61g_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	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)
F	SCOP2B Superfamily	EF-hand	8042162	3001983	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	EF-hand	8042162	3001983	SCOP2B (2022-06-29)
A	SCOP2 Family	S100 proteins	8029783	4000919	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	EF-hand	8042162	3001983	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	EF-hand	8042162	3001983	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-hand	8042162	3001983	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-hand	8042162	3001983	SCOP2B (2022-06-29)
G	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	S_100	e2h61B1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: S_100	ECOD (1.6)
F	S_100	e2h61F1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: S_100	ECOD (1.6)
H	S_100	e2h61H1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: S_100	ECOD (1.6)
A	S_100	e2h61A1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: S_100	ECOD (1.6)
E	S_100	e2h61E1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: S_100	ECOD (1.6)
C	S_100	e2h61C1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: S_100	ECOD (1.6)
D	S_100	e2h61D1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: S_100	ECOD (1.6)
G	S_100	e2h61G1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: S_100	ECOD (1.6)

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)
F	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
H	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)
E	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
C	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
D	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
G	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
A, B, E, F, H	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, B, E, F, H	PF00036	EF hand (EF-hand_1)	EF hand	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
C, D, G	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
C, D, G	PF00036	EF hand (EF-hand_1)	EF hand	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
A, B, E, F, H	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	metabolic process cellular process 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 metabolic process cellular process 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 positive regulation of signaling developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development 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 axonogenesis axon development cell morphogenesis involved in neuron differentiation cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation 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 regulation of biological quality regulation of developmental process regulation of cell differentiation positive regulation of neuron differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of neuron differentiation cell adhesion	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen extracellular region ruffle cell projection cell leading edge plasma membrane bounded cell projection perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body extracellular space
C, D, G	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	metabolic process cellular process 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 metabolic process cellular process 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 positive regulation of signaling developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development 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 axonogenesis axon development cell morphogenesis involved in neuron differentiation cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation 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 regulation of biological quality regulation of developmental process regulation of cell differentiation positive regulation of neuron differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of neuron differentiation cell adhesion	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen extracellular region ruffle cell projection cell leading edge plasma membrane bounded cell projection perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, E, F, H	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 atypical teratoid rhabdoid tumor intracerebral hemorrhage brain cancer large cell medulloblastoma medulloblastoma breast cancer pneumocystosis depressive disorder schizophrenia fetal methylmercury syndrome major depressive disorder breast carcinoma pituitary cancer
C, D, G	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 atypical teratoid rhabdoid tumor intracerebral hemorrhage brain cancer large cell medulloblastoma 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
C, D, G	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.