5W1F | pdb_00005w1f

Crystal structure of Ni(II)- and Ca(II)-bound human calprotectin

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	d5w1fa_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	Calcyclin (S100)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5w1fc_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	Calcyclin (S100)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth G]	d5w1fg_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	Calcyclin (S100)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth E]	d5w1fe_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	Calcyclin (S100)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5w1fb_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5w1fd_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth H]	d5w1fh_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth F]	d5w1ff_	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)
A	SCOP2B Superfamily	EF-hand	8033747	3001983	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-hand	8033747	3001983	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	EF-hand	8033747	3001983	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	EF-hand	8033747	3001983	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-hand	8033752	3001983	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-hand	8033752	3001983	SCOP2B (2022-06-29)
F [auth H]	SCOP2B Superfamily	EF-hand	8033752	3001983	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	EF-hand	8033752	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)
A	NUC	e5w1fA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: NUC	ECOD (v294.1)
C	NUC	e5w1fC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: NUC	ECOD (v294.1)
E [auth G]	NUC	e5w1fG1	A: a/b three-layered sandwiches	X: HAD domain-like	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: NUC	ECOD (v294.1)
G [auth E]	NUC	e5w1fE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: NUC	ECOD (v294.1)
B	Pyr_redox_2	e5w1fB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Pyr_redox_2	ECOD (v294.1)
D	S_100, EF-hand_7	e5w1fD1	A: a/b three-layered sandwiches	X: EF-hand	H: EF-hand-related	T: EF-hand	F: S_100, EF-hand_7	ECOD (v294.1)
F [auth H]	Pyr_redox_2	e5w1fH1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Pyr_redox_2	ECOD (v294.1)
H [auth F]	NUC	e5w1fF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: NUC	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
E [auth G]	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
G [auth E]	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
B	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)
F [auth H]	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
H [auth F]	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, C, E [auth G], G [auth E]	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, D, F [auth H], H [auth F]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E [auth G], G [auth E]	Protein S100-A8	arachidonate binding fatty acid binding icosanoid binding organic acid binding binding long-chain fatty acid binding icosatetraenoic acid binding ion binding anion binding lipid binding carboxylic acid binding small molecule binding monocarboxylic acid binding cytoskeletal protein binding arachidonate binding fatty acid binding icosanoid binding organic acid binding binding long-chain fatty acid binding icosatetraenoic acid binding ion binding anion binding lipid binding carboxylic acid binding small molecule binding monocarboxylic acid binding cytoskeletal protein binding microtubule binding protein binding tubulin binding cation binding calcium ion binding metal ion binding Toll-like receptor 4 binding signaling receptor binding Toll-like receptor binding RAGE receptor binding calcium-dependent protein binding transition metal ion binding zinc ion binding	regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism endothelial cell migration cell migration cell motility cell chemotaxis cellular response to stimulus chemotaxis neutrophil chemotaxis neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis response to chemical myeloid leukocyte migration leukocyte chemotaxis locomotion apoptotic process cell death programmed cell death biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont response to biotic stimulus defense response to other organism innate immune response response to external biotic stimulus defense response to bacterium response to bacterium leukocyte migration involved in inflammatory response positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway toll-like receptor signaling pathway regulation of signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of innate immune response regulation of pattern recognition receptor signaling pathway activation of innate immune response regulation of immune response regulation of toll-like receptor signaling pathway activation of immune response regulation of response to biotic stimulus signaling immune response-regulating signaling pathway regulation of signaling positive regulation of innate immune response regulation of cell communication developmental process multicellular organismal process cellular developmental process astrocyte differentiation cell development nervous system development glial cell development multicellular organism development neurogenesis astrocyte development central nervous system development gliogenesis glial cell differentiation cell differentiation anatomical structure development system development cell-cell signaling autocrine signaling peptidyl-cysteine modification primary metabolic process peptidyl-cysteine S-nitrosylation macromolecule modification peptidyl-amino acid modification protein metabolic process macromolecule metabolic process protein modification process protein nitrosylation neutrophil aggregation cell adhesion cell-cell adhesion leukocyte cell-cell adhesion leukocyte aggregation peptide transport peptide secretion localization secretion transport establishment of localization response to metal ion response to zinc ion positive regulation of cell communication positive regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction positive regulation of apoptotic signaling pathway regulation of intracellular signal transduction intrinsic apoptotic signaling pathway positive regulation of cellular process positive regulation of programmed cell death regulation of apoptotic process positive regulation of intracellular signal transduction positive regulation of apoptotic process apoptotic signaling pathway positive regulation of intrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway positive regulation of signaling regulation of growth regulation of cellular component organization growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular component organization or biogenesis chronic inflammatory response positive regulation of peptide secretion regulation of localization regulation of peptide secretion regulation of transport regulation of peptide transport regulation of secretion positive regulation of secretion positive regulation of transport regulation of cytoskeleton organization regulation of organelle organization organelle organization cytoskeleton organization response to alcohol response to oxygen-containing compound response to ethanol defense response to fungus response to fungus response to lipid response to lipopolysaccharide response to molecule of bacterial origin	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton membraneless organelle intracellular membraneless organelle S100A8 complex protein-containing complex intermediate filament cytoskeleton cell periphery plasma membrane membrane extracellular matrix external encapsulating structure calprotectin complex vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen cytoplasmic vesicle organelle lumen secretory granule secretory vesicle nucleus
B, D, F [auth H], H [auth F]	Protein S100-A9	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding antioxidant activity Toll-like receptor 4 binding protein binding signaling receptor binding Toll-like receptor binding arachidonate binding fatty acid binding icosanoid binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding antioxidant activity Toll-like receptor 4 binding protein binding signaling receptor binding Toll-like receptor binding arachidonate binding fatty acid binding icosanoid binding organic acid binding long-chain fatty acid binding icosatetraenoic acid binding anion binding lipid binding carboxylic acid binding monocarboxylic acid binding cytoskeletal protein binding microtubule binding tubulin binding RAGE receptor binding calcium-dependent protein binding transition metal ion binding zinc ion binding	regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation 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 process cellular component organization or biogenesis regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation 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 process cellular component organization or biogenesis positive regulation of cellular process regulation of immune effector process multicellular organismal process regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus response to biotic stimulus regulation of respiratory burst involved in inflammatory response response to stress regulation of response to stress innate immune response regulation of immune system process regulation of multicellular organismal process response to external biotic stimulus regulation of respiratory burst production of molecular mediator involved in inflammatory response respiratory burst involved in defense response defense response immune response response to other organism regulation of innate immune response defense response to symbiont response to external stimulus regulation of inflammatory response immune effector process respiratory burst regulation of response to stimulus immune system process defense response to other organism respiratory burst involved in inflammatory response regulation of immune response metabolic process inflammatory response regulation of metabolic process positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response positive regulation of defense response chronic inflammatory response catabolic process autophagy process utilizing autophagic mechanism endothelial cell migration cell migration cell motility cell chemotaxis cellular response to stimulus chemotaxis neutrophil chemotaxis neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis granulocyte chemotaxis response to chemical myeloid leukocyte migration leukocyte chemotaxis locomotion apoptotic process cell death programmed cell death signaling cell-cell signaling cell communication regulation of cytoskeleton organization regulation of organelle organization organelle organization cytoskeleton organization defense response to bacterium response to bacterium leukocyte migration involved in inflammatory response positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway toll-like receptor signaling pathway regulation of signal transduction immune response-activating signaling pathway positive regulation of immune response signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of pattern recognition receptor signaling pathway activation of innate immune response regulation of toll-like receptor signaling pathway activation of immune response immune response-regulating signaling pathway regulation of signaling positive regulation of innate immune response regulation of cell communication developmental process cellular developmental process astrocyte differentiation cell development nervous system development glial cell development multicellular organism development neurogenesis astrocyte development central nervous system development gliogenesis glial cell differentiation cell differentiation anatomical structure development system development autocrine signaling regulation of neuron projection development positive regulation of cellular component organization cell projection organization neuron projection development neuron differentiation positive regulation of neuron projection development positive regulation of cell projection organization plasma membrane bounded cell projection organization regulation of cell projection organization generation of neurons neuron development regulation of plasma membrane bounded cell projection organization neutrophil aggregation cell adhesion cell-cell adhesion leukocyte cell-cell adhesion leukocyte aggregation peptidyl-cysteine modification primary metabolic process peptidyl-cysteine S-nitrosylation peptidyl-cysteine S-trans-nitrosylation macromolecule modification peptidyl-amino acid modification protein metabolic process macromolecule metabolic process protein modification process protein nitrosylation humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide defense response to fungus response to fungus positive regulation of cell communication positive regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction positive regulation of apoptotic signaling pathway regulation of intracellular signal transduction intrinsic apoptotic signaling pathway positive regulation of programmed cell death regulation of apoptotic process positive regulation of intracellular signal transduction positive regulation of apoptotic process apoptotic signaling pathway positive regulation of intrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway positive regulation of signaling	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex transmembrane transporter complex S100A9 complex membrane protein complex transporter complex extracellular matrix external encapsulating structure calprotectin complex intracellular organelle cytoskeleton membraneless organelle intracellular membraneless organelle vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen cytoplasmic vesicle organelle lumen secretory granule secretory vesicle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E [auth G], G [auth E]	Pharos: P05109	acute myeloid leukemia keloid atopic eczema contact dermatitis gastric cancer interstitial cystitis large cell medulloblastoma lung carcinoma Mammary Carcinoma, Animal myopathy adrenal cortex adenoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous carcinoma breast carcinoma acute myeloid leukemia keloid atopic eczema contact dermatitis gastric cancer interstitial cystitis large cell medulloblastoma lung carcinoma Mammary Carcinoma, Animal myopathy adrenal cortex adenoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous carcinoma breast carcinoma pituitary cancer tuberculosis dermatitis, atopic gastritis invasive ductal breast carcinoma lung adenocarcinoma lymphoplasmacytic lymphoma mammary neoplasms, animal nasopharyngeal carcinoma ovarian cancer B-cell chronic lymphocytic leukemia pancreatic intraductal papillary-mucinous neoplasm congestive heart failure psoriasis Crohn disease type 2 diabetes mellitus dermatomyositis esophageal adenocarcinoma glioblastoma lung cancer MALT lymphoma medulloblastoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma breast cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Sjogren syndrome cutaneous lupus erythematosus ulcerative colitis duodenal ulcer
B, D, F [auth H], H [auth F]	Pharos: P06702	malignant colon neoplasm adult acute respiratory distress syndrome keloid Liver Cirrhosis, Experimental nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sinusitis B-cell chronic lymphocytic leukemia colonic neoplasm cystic fibrosis gastric carcinoma lung cancer MALT lymphoma osteosarcoma psoriasis malignant colon neoplasm adult acute respiratory distress syndrome keloid Liver Cirrhosis, Experimental nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sinusitis B-cell chronic lymphocytic leukemia colonic neoplasm cystic fibrosis gastric carcinoma lung cancer MALT lymphoma osteosarcoma psoriasis tuberculosis asthma benign colon neoplasm Crohn disease dermatomyositis glioblastoma large cell medulloblastoma lung carcinoma myopathy ovarian cancer schizophrenia ulcerative colitis atopic eczema breast carcinoma cutaneous lupus erythematosus esophageal adenocarcinoma interstitial cystitis

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.