3IKQ | pdb_00003ikq

Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D

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	d3ikqc2	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	C-type lectin domain	Surfactant protein, lectin domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3ikqc1	Coiled coil proteins	Parallel coiled-coil	Triple coiled coil domain of C-type lectins	Triple coiled coil domain of C-type lectins	Surfactant protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ikqb2	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	C-type lectin domain	Surfactant protein, lectin domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ikqb1	Coiled coil proteins	Parallel coiled-coil	Triple coiled coil domain of C-type lectins	Triple coiled coil domain of C-type lectins	Surfactant protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ikqa2	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	C-type lectin domain	Surfactant protein, lectin domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ikqa1	Coiled coil proteins	Parallel coiled-coil	Triple coiled coil domain of C-type lectins	Triple coiled coil domain of C-type lectins	Surfactant protein	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	C-type lectin-like	8039230	3001261	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-type lectin-like	8039230	3001261	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C-type lectin-like	8039230	3001261	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)
C	ATP-synt_ab_N	e3ikqC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: ATP-synt_ab_N	ECOD (v294.1)
B	ERG4_ERG24	e3ikqB2	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (v294.1)
A	ERG4_ERG24	e3ikqA2	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
B	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
A	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00059	Lectin C-type domain (Lectin_C)	Lectin C-type domain	This family includes both long and short form C-type	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Pulmonary surfactant-associated protein D	binding carbohydrate binding identical protein binding protein binding	multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of interleukin-2 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of interleukin-2 production regulation of biological process negative regulation of metabolic process biological regulation multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of interleukin-2 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of interleukin-2 production regulation of biological process negative regulation of metabolic process biological regulation interleukin-2 production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process multicellular organismal-level homeostasis chemical homeostasis homeostatic process multicellular organismal-level chemical homeostasis surfactant homeostasis reactive oxygen species metabolic process respiratory gaseous exchange by respiratory system biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus negative regulation of lymphocyte proliferation regulation of leukocyte activation regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of immune system process regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of leukocyte activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport positive regulation of biological process vesicle-mediated transport cellular component organization localization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis defense response to bacterium response to bacterium cell chemotaxis cellular response to stimulus chemotaxis macrophage chemotaxis macrophage migration leukocyte migration cellular response to chemical stimulus taxis response to chemical mononuclear cell migration myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion developmental process tube development animal organ development respiratory tube development multicellular organism development anatomical structure development lung development respiratory system development lung alveolus development system development receptor-mediated endocytosis	protein-containing complex collagen trimer membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle endocytic vesicle endosome protein-containing complex collagen trimer membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle endocytic vesicle endosome endomembrane system late endosome multivesicular body lytic vacuole vacuole lysosome organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane extracellular region clathrin-coated endocytic vesicle clathrin-coated vesicle coated vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR008160	Collagen triple helix repeat	Repeat
A, B, C	IPR051077	Calcium-dependent Lectin	Family
A, B, C	IPR016187	C-type lectin fold	Homologous Superfamily
A, B, C	IPR001304	C-type lectin-like	Domain
A, B, C	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
A, B, C	IPR015097	Lung surfactant protein D coiled-coil trimerisation	Domain
A, B, C	IPR018378	C-type lectin, conserved site	Conserved Site
A, B, C	IPR033990	Collectin, C-type lectin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P35247	chronic obstructive pulmonary disease rheumatoid arthritis acute lung injury interstitial lung disease lung cancer malignant ependymoma pancreatic intraductal papillary-mucinous carcinoma Chronic Airflow Obstruction cutaneous lupus erythematosus lung adenocarcinoma lung carcinoma pneumonia facioscapulohumeral muscular dystrophy lung benign neoplasm non-small cell lung carcinoma

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.