8DEW | pdb_00008dew

Cryo-electron microscopy structure of Neisseria gonorrhoeae multidrug efflux pump MtrD with LL-37 complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	PHF5	e8dewC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PHF5	ECOD (v294.1)
B	PHF5	e8dewB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PHF5	ECOD (v294.1)
A	PHF5	e8dewA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PHF5	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.2090.10	Alpha Beta	2-Layer Sandwich	Multidrug efflux transporter AcrB TolC docking domain	DN and DC subdomains	CATH (utative)
B	3.30.70.1430	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Multidrug efflux transporter AcrB pore domain	CATH (utative)
A	3.30.2090.10	Alpha Beta	2-Layer Sandwich	Multidrug efflux transporter AcrB TolC docking domain	DN and DC subdomains	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF12153	LPS binding domain of CAP18 (C terminal) (CAP18_C)	LPS binding domain of CAP18 (C terminal)	This domain family is found in eukaryotes, and is approximately 30 amino acids in length, and the family is found in association with Pfam:PF00666. CAP18 is a protein which is derived from rabbit granulocytes. It has two domains, an N terminal DUF an ...	This domain family is found in eukaryotes, and is approximately 30 amino acids in length, and the family is found in association with Pfam:PF00666. CAP18 is a protein which is derived from rabbit granulocytes. It has two domains, an N terminal DUF and a C terminal Gram negative LPS binding domain. This domain is the C terminal domain.	Domain
A, B, C	PF00873	AcrB/AcrD/AcrF family (ACR_tran)	AcrB/AcrD/AcrF family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	Antibacterial peptide LL-37	binding lipid binding lipopolysaccharide binding carbohydrate derivative binding	icosanoid metabolic process leukotriene metabolic process oxoacid metabolic process small molecule biosynthetic process leukotriene biosynthetic process carboxylic acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process icosanoid biosynthetic process small molecule metabolic process metabolic process cellular process icosanoid metabolic process leukotriene metabolic process oxoacid metabolic process small molecule biosynthetic process leukotriene biosynthetic process carboxylic acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process icosanoid biosynthetic process small molecule metabolic process metabolic process cellular process cellular response to nitrogen compound cellular response to stimulus biological process involved in interspecies interaction between organisms response to stimulus response to other organism cellular response to peptidoglycan response to oxygen-containing compound response to external stimulus response to nitrogen compound cellular response to molecule of bacterial origin cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to bacterium response to chemical response to external biotic stimulus response to molecule of bacterial origin response to peptidoglycan regulation of humoral immune response regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus humoral immune response regulation of response to external stimulus positive regulation of biological process antimicrobial humoral response positive regulation of response to stimulus positive regulation of humoral immune response positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress regulation of immune system process positive regulation of immune system process regulation of antimicrobial humoral response regulation of biological process defense response immune response biological regulation defense response to symbiont positive regulation of antimicrobial humoral response regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response regulation of immune response regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death cellular component organization primary metabolic process protein metabolic process macromolecule metabolic process cellular component organization or biogenesis supramolecular fiber organization amyloid fibril formation neutrophil activation multicellular organismal process cell activation myeloid leukocyte activation granulocyte activation leukocyte activation antibacterial humoral response defense response to bacterium innate immune response response to butyrate response to lipid cellular response to butyrate response to fatty acid cellular response to fatty acid cellular response to lipid cellular response to dsRNA cellular response to exogenous dsRNA response to dsRNA response to exogenous dsRNA cellular response to lipopolysaccharide response to lipopolysaccharide response to hexose response to monosaccharide response to carbohydrate response to glucose regulation of monocyte chemotactic protein-1 production positive regulation of monocyte chemotactic protein-1 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process monocyte chemotactic protein-1 production positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of chemokine production regulation of gene expression positive regulation of gene expression chemokine production positive regulation of chemokine production positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process interleukin-1 production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production positive regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production production of molecular mediator involved in inflammatory response arachidonate metabolite production involved in inflammatory response prostaglandin production involved in inflammatory response inflammatory response cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation response to peptide cellular response to tumor necrosis factor response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor developmental process anatomical structure morphogenesis odontogenesis of dentin-containing tooth dentinogenesis anatomical structure formation involved in morphogenesis anatomical structure development odontogenesis animal organ development animal organ morphogenesis positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization cell communication localization carbohydrate homeostasis establishment of localization in cell positive regulation of insulin secretion involved in cellular response to glucose stimulus positive regulation of insulin secretion intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region intracellular glucose homeostasis protein secretion establishment of localization regulation of protein secretion regulation of secretion cellular response to carbohydrate stimulus chemical homeostasis glucose homeostasis positive regulation of protein localization insulin secretion involved in cellular response to glucose stimulus cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport signaling homeostatic process positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion signal release cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus positive regulation of peptide secretion regulation of signaling regulation of transport secretion regulation of peptide transport regulation of establishment of protein localization export from cell cell-cell signaling cellular response to glucose stimulus regulation of protein transport positive regulation of protein secretion peptide transport cellular homeostasis positive regulation of transport regulation of cellular localization protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization regulation of insulin secretion involved in cellular response to glucose stimulus hormone transport regulation of cell communication insulin secretion positive regulation of signaling response to interleukin-6 cellular response to interleukin-6 innate immune response in mucosa mucosal immune response organ or tissue specific immune response regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process multicellular organism development tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development system development regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development positive regulation of vasculature development regulation of angiogenesis antimicrobial humoral immune response mediated by antimicrobial peptide cytolysis granulocyte macrophage colony-stimulating factor production positive regulation of protein metabolic process positive regulation of granulocyte macrophage colony-stimulating factor production regulation of primary metabolic process regulation of granulocyte macrophage colony-stimulating factor production regulation of protein metabolic process defense response to Gram-negative bacterium regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production cellular response to interleukin-1 response to interleukin-1 macrophage inflammatory protein-1 alpha production regulation of macrophage inflammatory protein 1 alpha production positive regulation of macrophage inflammatory protein 1 alpha production defense response to Gram-positive bacterium	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure tertiary granule lumen membrane-enclosed lumen intracellular vesicle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure tertiary granule lumen membrane-enclosed lumen intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen tertiary granule intracellular organelle organelle lumen cytoplasmic vesicle secretory granule secretory vesicle cytoplasm vesicle lumen cytoplasmic vesicle lumen secretory granule lumen specific granule lumen specific granule cell projection
A, B, C	Efflux pump membrane transporter	efflux transmembrane transporter activity transporter activity transmembrane transporter activity xenobiotic transmembrane transporter activity	response to stimulus response to chemical response to toxic substance	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR046350	Cystatin superfamily	Homologous Superfamily
D	IPR001894	Cathelicidin-like	Family
D	IPR022746	Cathelicidin, antimicrobial peptide, C-terminal	Domain
D	IPR018216	Cathelicidin, conserved site	Conserved Site
A, B, C	IPR001036	Acriflavin resistance protein	Family
A, B, C	IPR004764	Multidrug resistance protein MdtF-like	Family
A, B, C	IPR027463	Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains	Homologous Superfamily
A, B, C	IPR000731	Sterol-sensing domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	Pharos: P49913	psoriasis breast cancer lung adenocarcinoma chronic obstructive pulmonary disease lymphoplasmacytic lymphoma rosacea heart disease osteosarcoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Transmembrane	Alpha-helical polytopic	Resistance-nodulation-cell division	Heavy metal efflux family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D	MemProtMD	Annotated as membrane protein by MemProtMD

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.

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