6QZH | pdb_00006qzh

Structure of the human CC Chemokine Receptor 7 in complex with the intracellular allosteric antagonist Cmp2105 and the insertion protein Sialidase NanA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Sialidases	8052060	3001607	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	BNR_2,7tm_1_1	e6qzhA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: BNR_2,7tm_1_1	ECOD (1.6)
A	7tm_1_1	e6qzhA2	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: 7tm_1_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02012	BNR/Asp-box repeat (BNR)	BNR/Asp-box repeat	-	Repeat
A	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GC ...	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	C-C chemokine receptor type 7,Sialidase A,C-C chemokine receptor type 7	hydrolase activity, acting on glycosyl bonds alpha-sialidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity exo-alpha-sialidase activity catalytic activity chemokine (C-C motif) ligand 21 binding C-C chemokine binding protein binding binding chemokine binding cytokine binding G protein-coupled chemoattractant receptor activity C-C motif chemokine 19 receptor activity hydrolase activity, acting on glycosyl bonds alpha-sialidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity exo-alpha-sialidase activity catalytic activity chemokine (C-C motif) ligand 21 binding C-C chemokine binding protein binding binding chemokine binding cytokine binding G protein-coupled chemoattractant receptor activity C-C motif chemokine 19 receptor activity C-C chemokine receptor activity molecular transducer activity chemokine receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity cytokine receptor activity immune receptor activity chemokine (C-C motif) ligand 19 binding C-C motif chemokine 21 receptor activity	carbohydrate metabolic process catabolic process oligosaccharide catabolic process oligosaccharide metabolic process carbohydrate catabolic process primary metabolic process metabolic process cellular process membrane lipid metabolic process sphingolipid catabolic process ceramide metabolic process ganglioside catabolic process carbohydrate derivative catabolic process glycosphingolipid catabolic process carbohydrate metabolic process catabolic process oligosaccharide catabolic process oligosaccharide metabolic process carbohydrate catabolic process primary metabolic process metabolic process cellular process membrane lipid metabolic process sphingolipid catabolic process ceramide metabolic process ganglioside catabolic process carbohydrate derivative catabolic process glycosphingolipid catabolic process lipid catabolic process glycolipid metabolic process glycosphingolipid metabolic process liposaccharide metabolic process carbohydrate derivative metabolic process sphingolipid metabolic process membrane lipid catabolic process glycolipid catabolic process ceramide catabolic process amide metabolic process ganglioside metabolic process lipid metabolic process developmental process myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development mononuclear cell differentiation myeloid cell differentiation cell differentiation anatomical structure development dendritic cell differentiation mature conventional dendritic cell differentiation leukocyte differentiation thymic T cell selection multicellular organismal process cell activation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process negative thymic T cell selection T cell differentiation negative T cell selection T cell selection regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization cell projection organization positive regulation of biological process plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization pseudopodium assembly cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of cellular process regulation of biological process plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly biological regulation regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly positive regulation of pseudopodium assembly regulation of pseudopodium assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly pseudopodium organization regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion cell adhesion cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion cell chemotaxis cellular response to stimulus chemotaxis dendritic cell chemotaxis response to stimulus response to external stimulus leukocyte migration dendritic cell migration myeloid dendritic cell chemotaxis cellular response to chemical stimulus taxis response to chemical mononuclear cell migration myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion regulation of biosynthetic process regulation of type II interferon production type II interferon production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process cytokine production regulation of cytokine production regulation of macromolecule biosynthetic process regulation of multicellular organismal process macromolecule metabolic process regulation of metabolic process regulation of humoral immune response humoral immune response immune response positive regulation of response to stimulus positive regulation of humoral immune response regulation of response to stimulus positive regulation of immune response regulation of immune response regulation of immune system process positive regulation of immune system process positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction positive regulation of T cell receptor signaling pathway signaling regulation of antigen receptor-mediated signaling pathway regulation of signal transduction cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction regulation of signaling cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway regulation of T cell receptor signaling pathway T cell receptor signaling pathway regulation of cell communication antigen receptor-mediated signaling pathway activation of immune response positive regulation of antigen receptor-mediated signaling pathway positive regulation of signaling intracellular signal transduction positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade lymphocyte migration into lymphoid organs lymphocyte migration lymphocyte migration into lymph node ruffle organization regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity regulation of protein kinase activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process positive regulation of locomotion regulation of cell motility regulation of locomotion positive regulation of cell motility regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion positive regulation of T cell costimulation leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell-cell adhesion positive regulation of leukocyte activation regulation of cell-cell adhesion positive regulation of T cell activation regulation of T cell costimulation regulation of T cell activation lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process T cell costimulation regulation of lymphocyte activation regulation of interleukin-1 production interleukin-1 production regulation of interleukin-1 beta production interleukin-1 beta production response to nitric oxide response to oxygen-containing compound response to nitrogen compound positive regulation of cytosolic calcium ion concentration regulation of biological quality positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells positive regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of dendritic cell chemotaxis regulation of response to external stimulus positive regulation of chemotaxis positive regulation of cell migration positive regulation of response to external stimulus regulation of cell migration positive regulation of mononuclear cell migration regulation of mononuclear cell migration regulation of dendritic cell chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis regulation of chemotaxis immunological synapse formation positive regulation of glycoprotein metabolic process positive regulation of macromolecule biosynthetic process positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation positive regulation of biosynthetic process cell recognition regulation of glycoprotein biosynthetic process positive regulation of glycoprotein biosynthetic process carbohydrate derivative biosynthetic process cell-cell recognition glycoprotein biosynthetic process glycoprotein metabolic process regulation of glycoprotein metabolic process positive regulation of acute inflammatory response to antigenic stimulus regulation of defense response regulation of acute inflammatory response to antigenic stimulus positive regulation of acute inflammatory response inflammatory response to antigenic stimulus positive regulation of hypersensitivity positive regulation of inflammatory response response to stress regulation of response to stress acute inflammatory response hypersensitivity regulation of hypersensitivity defense response regulation of inflammatory response to antigenic stimulus regulation of inflammatory response acute inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus positive regulation of defense response regulation of acute inflammatory response inflammatory response regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production positive regulation of gene expression positive regulation of cytokine production positive regulation of neutrophil chemotaxis neutrophil migration granulocyte migration positive regulation of granulocyte chemotaxis regulation of neutrophil chemotaxis regulation of neutrophil migration neutrophil chemotaxis regulation of granulocyte chemotaxis positive regulation of neutrophil migration granulocyte chemotaxis regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction calcium-mediated signaling regulation of dendritic cell dendrite assembly dendritic cell dendrite assembly regulation of leukocyte apoptotic process dendritic cell apoptotic process negative regulation of dendritic cell apoptotic process negative regulation of programmed cell death leukocyte apoptotic process regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of leukocyte apoptotic process negative regulation of cellular process regulation of dendritic cell apoptotic process apoptotic process programmed cell death positive regulation of immunological synapse formation regulation of immunological synapse formation response to ketone response to prostaglandin response to lipid response to hormone response to endogenous stimulus response to alcohol response to prostaglandin E positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of cellular component size regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of protein polymerization protein-containing complex assembly actin filament-based process regulation of actin filament polymerization protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin cytoskeleton organization actin filament polymerization protein-containing complex organization positive regulation of cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization positive regulation of supramolecular fiber organization regulation of organelle organization organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of actin filament polymerization cytoskeleton organization regulation of anatomical structure size regulation of localization cellular localization inorganic ion homeostasis intracellular calcium ion homeostasis transport monoatomic ion transmembrane transport calcium ion homeostasis negative regulation of sequestering of calcium ion calcium ion transport metal ion transport maintenance of location in cell monoatomic cation transmembrane transport localization intracellular monoatomic cation homeostasis monoatomic ion homeostasis monoatomic ion transport intracellular chemical homeostasis monoatomic cation homeostasis monoatomic cation transport regulation of sequestering of calcium ion intracellular monoatomic ion homeostasis calcium ion transmembrane import into cytosol sequestering of calcium ion inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol cellular homeostasis chemical homeostasis calcium ion transmembrane transport filopodium assembly regulation of filopodium assembly positive regulation of filopodium assembly establishment of lymphocyte polarity establishment of T cell polarity establishment or maintenance of cell polarity establishment of cell polarity negative regulation of interleukin-12 production negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cytokine production negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process regulation of dendritic cell antigen processing and presentation positive regulation of dendritic cell antigen processing and presentation positive regulation of antigen processing and presentation antigen processing and presentation regulation of antigen processing and presentation dendritic cell antigen processing and presentation G protein-coupled receptor signaling pathway biological process involved in interspecies interaction between organisms response to other organism response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin response to peptide response to cytokine cellular response to cytokine stimulus	cellular anatomical structure membrane extracellular region membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm cell periphery cell surface plasma membrane external side of plasma membrane side of membrane cellular anatomical structure membrane extracellular region membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm cell periphery cell surface plasma membrane external side of plasma membrane side of membrane mitochondrion

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001791	Laminin G domain	Domain
A	IPR011040	Sialidase	Domain
A	IPR049964	Sialidase A repeat	Repeat
A	IPR023364	Trans-sialidase, domain 3	Homologous Superfamily
A	IPR036278	Sialidase superfamily	Homologous Superfamily
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR004124	Glycoside hydrolase, family 33, N-terminal	Domain
A	IPR005877	YSIRK Gram-positive signal peptide	Domain
A	IPR026856	Sialidase family	Family
A	IPR019931	LPXTG cell wall anchor domain	Domain
A	IPR001718	CC chemokine receptor 7	Family
A	IPR000355	Chemokine receptor family	Family
A	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A	IPR050119	C-C chemokine receptor type 1-9-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P32248	status epilepticus adult T-cell leukemia/lymphoma psoriasis Sjogren syndrome tuberculosis acute T cell leukemia Anhedonia B-cell chronic lymphocytic leukemia invasive ductal breast carcinoma osteosarcoma sarcoidosis ulcerative colitis atopic eczema cancer cutaneous lupus erythematosus status epilepticus adult T-cell leukemia/lymphoma psoriasis Sjogren syndrome tuberculosis acute T cell leukemia Anhedonia B-cell chronic lymphocytic leukemia invasive ductal breast carcinoma osteosarcoma sarcoidosis ulcerative colitis atopic eczema cancer cutaneous lupus erythematosus hematologic disease lung cancer allergic rhinitis autoimmune disease common variable immunodeficiency ductal breast carcinoma in situ interstitial cystitis

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	G-protein coupled receptors, family A

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	CCR7 chemokine receptor in complex with Cmp2105

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.