2D39 | pdb_00002d39

Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of human M-ficolin Fibrinogen-like Domain

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)
C	d2d39c_	Alpha and beta proteins (a+b)	Fibrinogen C-terminal domain-like	Fibrinogen C-terminal domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2d39b1	Alpha and beta proteins (a+b)	Fibrinogen C-terminal domain-like	Fibrinogen C-terminal domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2d39b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2d39a1	Alpha and beta proteins (a+b)	Fibrinogen C-terminal domain-like	Fibrinogen C-terminal domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2d39a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
C	SCOP2B Superfamily	Fibrinogen C-terminal domain-like	8070776	3001395	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Fibrinogen C-terminal domain-like	8070776	3001395	SCOP2B (2022-06-29)
A	SCOP2 Family	Fibrinogen C-terminal domain-like	8070775	4002544	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Fibrinogen C-terminal domain-like	8070776	3001395	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)
C	Sigma70_r4_2	e2d39C1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (develop294)
B	Sigma70_r4_2	e2d39B1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Sigma70_r4_2	ECOD (develop294)
A	Transketolase_C	e2d39A1	A: alpha bundles	X: Profilin-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Transketolase_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.90.215.10	Alpha Beta	Alpha-Beta Complex	Gamma Fibrinogen	Chain A, domain 1	CATH (4.3.0)
C	4.10.530.10	Few Secondary Structures	Irregular	Gamma-fibrinogen Carboxyl Terminal Fragment	domain 2	CATH (4.3.0)
B	3.90.215.10	Alpha Beta	Alpha-Beta Complex	Gamma Fibrinogen	Chain A, domain 1	CATH (4.3.0)
B	4.10.530.10	Few Secondary Structures	Irregular	Gamma-fibrinogen Carboxyl Terminal Fragment	domain 2	CATH (4.3.0)
A	3.90.215.10	Alpha Beta	Alpha-Beta Complex	Gamma Fibrinogen	Chain A, domain 1	CATH (4.3.0)
A	4.10.530.10	Few Secondary Structures	Irregular	Gamma-fibrinogen Carboxyl Terminal Fragment	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00147	Fibrinogen beta and gamma chains, C-terminal globular domain (Fibrinogen_C)	Fibrinogen beta and gamma chains, C-terminal globular domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Ficolin-1	sialic acid binding organic acid binding binding ion binding anion binding carboxylic acid binding carbohydrate derivative binding small molecule binding protein binding signaling receptor binding molecular transducer activity pattern recognition receptor activity signaling receptor activity antigen binding sialic acid binding organic acid binding binding ion binding anion binding carboxylic acid binding carbohydrate derivative binding small molecule binding protein binding signaling receptor binding molecular transducer activity pattern recognition receptor activity signaling receptor activity antigen binding carbohydrate binding G protein-coupled receptor binding cation binding metal ion binding	cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway response to biotic stimulus 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 cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway response to biotic stimulus 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 biological process immune response response to other organism immune response-activating cell surface receptor signaling pathway regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus signaling positive regulation of biological process innate immune response activating cell surface receptor signaling pathway positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus cell surface pattern recognition receptor signaling pathway positive regulation of innate immune response cell surface receptor signaling pathway defense response biological regulation defense response to symbiont immune system process cellular process import into cell transport establishment of localization vesicle-mediated transport phagocytosis, recognition localization phagocytosis cell recognition apoptotic cell clearance recognition of apoptotic cell endocytosis protein localization to cell surface macromolecule localization intracellular protein localization humoral immune response complement activation complement activation, lectin pathway immune effector process host-mediated suppression of symbiont invasion host-mediated perturbation of symbiont process modulation of process of another organism multicellular organismal process positive regulation of interleukin-8 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of multicellular organismal process positive regulation of cellular process regulation of biosynthetic process interleukin-8 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process regulation of interleukin-8 production G protein-coupled receptor signaling pathway regulation of immune effector process regulation of localization positive regulation of cellular component organization regulation of cellular component organization cellular component organization opsonization positive regulation of endocytosis positive regulation of immune effector process cellular component organization or biogenesis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of opsonization regulation of opsonization positive regulation of phagocytosis positive regulation of transport proteolysis primary metabolic process protein metabolic process	protein-containing complex collagen trimer cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane other organism part symbiont cell surface extracellular matrix external encapsulating structure membrane-bounded organelle protein-containing complex collagen trimer cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane other organism part symbiont cell surface extracellular matrix external encapsulating structure membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen organelle secretory granule secretory vesicle cytoplasm vesicle extracellular region vesicle lumen cytoplasmic vesicle lumen secretory granule lumen catalytic complex peptidase complex endopeptidase complex serine-type endopeptidase complex serine-type peptidase complex extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR008160	Collagen triple helix repeat	Repeat
A, B, C	IPR020837	Fibrinogen, conserved site	Conserved Site
A, B, C	IPR014716	Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1	Homologous Superfamily
A, B, C	IPR002181	Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain	Domain
A, B, C	IPR050373	Fibrinogen C-terminal domain-containing protein	Family
A, B, C	IPR036056	Fibrinogen-like, C-terminal	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: O00602	Liver Cirrhosis, Experimental Sjogren syndrome attention deficit hyperactivity disorder, inattentive type cutaneous lupus erythematosus lung adenocarcinoma MALT lymphoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis tuberculosis B-cell chronic lymphocytic leukemia interstitial cystitis lung cancer nephrosclerosis ovarian cancer Liver Cirrhosis, Experimental Sjogren syndrome attention deficit hyperactivity disorder, inattentive type cutaneous lupus erythematosus lung adenocarcinoma MALT lymphoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis tuberculosis B-cell chronic lymphocytic leukemia interstitial cystitis lung cancer nephrosclerosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sarcoidosis ulcerative colitis colorectal cancer lung carcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma periodontitis

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.