4M4D | pdb_00004m4d

Crystal structure of lipopolysaccharide binding protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4m4db1	Alpha and beta proteins (a+b)	Aha1/BPI domain-like	Bactericidal permeability-increasing protein, BPI	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d4m4da1	Alpha and beta proteins (a+b)	Aha1/BPI domain-like	Bactericidal permeability-increasing protein, BPI	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	His_biosynth	e4m4dB1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (develop294)
A	His_biosynth	e4m4dA1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.15.20.10	Alpha Beta	Super Roll	Bactericidal permeability-increasing protein	domain 2	CATH (4.3.0)
B	3.15.10.10	Alpha Beta	Super Roll	Bactericidal permeability-increasing protein	domain 1	CATH (4.3.0)
A	3.15.20.10	Alpha Beta	Super Roll	Bactericidal permeability-increasing protein	domain 2	CATH (4.3.0)
A	3.15.10.10	Alpha Beta	Super Roll	Bactericidal permeability-increasing protein	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01273	LBP / BPI / CETP family, N-terminal domain (LBP_BPI_CETP)	LBP / BPI / CETP family, N-terminal domain	-	Family
A, B	PF02886	LBP / BPI / CETP family, C-terminal domain (LBP_BPI_CETP_C)	LBP / BPI / CETP family, C-terminal domain	The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Lipopolysaccharide-binding protein	protein binding binding signaling receptor binding molecular transducer activity coreceptor activity signaling receptor activity lipid binding lipopolysaccharide binding carbohydrate derivative binding lipopeptide binding lipoteichoic acid binding	regulation of immune effector process multicellular organismal process positive regulation of response to biotic stimulus regulation of cellular process positive regulation of respiratory burst response to stimulus response to biotic stimulus positive regulation of metabolic process regulation of respiratory burst involved in inflammatory response positive regulation of immune response positive regulation of inflammatory response regulation of immune system process positive regulation of immune system process regulation of biological process regulation of immune effector process multicellular organismal process positive regulation of response to biotic stimulus regulation of cellular process positive regulation of respiratory burst response to stimulus response to biotic stimulus positive regulation of metabolic process regulation of respiratory burst involved in inflammatory response positive regulation of immune response positive regulation of inflammatory response regulation of immune system process positive regulation of immune system process regulation of biological process respiratory burst involved in defense response immune response response to other organism regulation of innate immune response response to external stimulus regulation of inflammatory response immune effector process regulation of response to stimulus defense response to other organism respiratory burst involved in inflammatory response positive regulation of defense response regulation of immune response positive regulation of multicellular organismal process metabolic process inflammatory response regulation of metabolic process regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus response to stress regulation of response to stress innate immune response regulation of multicellular organismal process positive regulation of immune effector process response to external biotic stimulus regulation of respiratory burst positive regulation of cellular process production of molecular mediator involved in inflammatory response positive regulation of innate immune response positive regulation of respiratory burst involved in inflammatory response defense response biological regulation defense response to symbiont respiratory burst immune system process cellular process import into cell transport establishment of localization vesicle-mediated transport phagocytosis, recognition opsonization localization phagocytosis cell recognition endocytosis cellular response to stimulus immune response-regulating cell surface receptor signaling pathway pattern recognition receptor signaling pathway cell communication immune response-activating signaling pathway signal transduction innate immune response-activating signaling pathway immune response-activating cell surface receptor signaling pathway activation of innate immune response activation of immune response signaling innate immune response activating cell surface receptor signaling pathway immune response-regulating signaling pathway cell surface pattern recognition receptor signaling pathway cell surface receptor signaling pathway regulation of macrophage activation positive regulation of macrophage activation regulation of leukocyte activation cell activation regulation of cell activation myeloid leukocyte activation leukocyte activation macrophage activation positive regulation of cell activation positive regulation of leukocyte activation regulation of tumor necrosis factor production negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process tumor necrosis factor superfamily cytokine production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction cell surface toll-like receptor signaling pathway positive regulation of pattern recognition receptor signaling pathway regulation of toll-like receptor 4 signaling pathway positive regulation of toll-like receptor 4 signaling pathway regulation of pattern recognition receptor signaling pathway regulation of signaling toll-like receptor 4 signaling pathway regulation of cell communication positive regulation of signaling regulation of localization regulation of cellular component organization positive regulation of cellular component organization positive regulation of membrane invagination cellular component organization positive regulation of endocytosis regulation of phagocytosis, engulfment membrane invagination cellular component organization or biogenesis plasma membrane invagination regulation of endocytosis membrane organization regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport phagocytosis, engulfment positive regulation of phagocytosis positive regulation of transport positive regulation of phagocytosis, engulfment regulation of membrane invagination interleukin-6 production positive regulation of macromolecule biosynthetic process positive regulation of interleukin-6 production regulation of interleukin-6 production positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of gene expression positive regulation of cytokine production response to lipid cellular response to lipopolysaccharide lipopolysaccharide-mediated signaling pathway cellular response to biotic stimulus response to bacterium response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to lipid response to molecule of bacterial origin positive regulation of locomotion regulation of cell motility positive regulation of chemotaxis positive regulation of cell migration positive regulation of neutrophil chemotaxis taxis cell migration chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte chemotaxis neutrophil migration granulocyte migration leukocyte migration positive regulation of granulocyte chemotaxis regulation of locomotion regulation of neutrophil chemotaxis regulation of neutrophil migration neutrophil chemotaxis regulation of granulocyte chemotaxis positive regulation of cell motility regulation of cell migration myeloid leukocyte migration cell motility locomotion cell chemotaxis positive regulation of leukocyte migration positive regulation of neutrophil migration regulation of chemotaxis granulocyte chemotaxis leukocyte chemotaxis positive regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production macrophage activation involved in immune response cell activation involved in immune response myeloid cell activation involved in immune response leukocyte activation involved in immune response regulation of chemokine production chemokine production positive regulation of chemokine production acute-phase response acute inflammatory response cellular response to lipoteichoic acid response to lipoteichoic acid leukocyte chemotaxis involved in inflammatory response leukocyte migration involved in inflammatory response lipopolysaccharide transport macromolecule localization lipid localization lipid transport carbohydrate derivative transport defense response to Gram-negative bacterium defense response to bacterium positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production regulation of membrane permeability regulation of biological quality defense response to Gram-positive bacterium detection of external biotic stimulus detection of molecule of bacterial origin detection of biotic stimulus detection of stimulus detection of chemical stimulus	cell surface cellular anatomical structure extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017943	Bactericidal permeability-increasing protein, alpha/beta domain superfamily	Homologous Superfamily
A, B	IPR017942	Lipid-binding serum glycoprotein, N-terminal	Domain
A, B	IPR030675	Lipid binding protein BPI/LBP	Family
A, B	IPR017954	Lipid-binding serum glycoprotein, conserved site	Conserved Site
A, B	IPR032942	BPI/LBP/Plunc family	Family
A, B	IPR001124	Lipid-binding serum glycoprotein, C-terminal	Domain

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.