4RWS | pdb_00004rws

Crystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI Community Target)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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
Membrane Protein Annotation: mpstruc

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth C]	d4rwsc_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	automated matches	HHV-8 (Human herpesvirus 8 strain GK18 ) [TaxId: 868565 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	Interleukin 8-like chemokines	8040942	3001955	SCOP2B (2022-06-29)
A	SCOP2 Family	Class A (rhodopsin) G protein-coupled receptor-like	8091229	4001858	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	G protein-coupled receptor-like	8091230	3000473	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	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)
B [auth C]	IL8	e4rwsC1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: IL8	ECOD (1.6)
A	7tm_1_1	e4rwsA1	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)
A	Phage_lysozyme_2	e4rwsA2	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Phage_lysozyme_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A	C-X-C chemokine receptor type 4/Endolysin chimeric protein	CXCR4	Homo sapiens (human)	CXCR4*01	R-LIKE-DOMAIN CXCR4 (Pr1-228), R-LIKE-DOMAIN CXCR4 (Pr231-319)	RPI	(CXCR4-LYZOZYME-CXCR4)	IMGT (202543-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	PF00048	Small cytokines (intecrine/chemokine), interleukin-8 like (IL8)	Small cytokines (intecrine/chemokine), interleukin-8 like	Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds.	Domain
A	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
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
B [auth C]	Viral macrophage inflammatory protein 2	binding molecular function activator activity signaling receptor binding G protein-coupled receptor binding signaling receptor activator activity protein binding cytokine receptor binding chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity chemokine receptor binding receptor ligand activity CXCR chemokine receptor binding	response to stimulus immune response immune system process	cellular anatomical structure extracellular region extracellular space protein-containing complex
A	C-X-C chemokine receptor type 4/Endolysin chimeric protein	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity molecular transducer activity coreceptor activity signaling receptor activity cytoskeletal protein binding myosin light chain binding protein binding binding myosin binding hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity molecular transducer activity coreceptor activity signaling receptor activity cytoskeletal protein binding myosin light chain binding protein binding binding myosin binding C-C chemokine binding chemokine binding cytokine binding G protein-coupled chemoattractant receptor activity C-X-C motif chemokine 12 receptor activity C-X-C chemokine receptor activity chemokine receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity cytokine receptor activity immune receptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding virus receptor activity exogenous protein binding C-C chemokine receptor activity ubiquitin binding ubiquitin-like protein binding actin binding	defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process cellular process macromolecule metabolic process symbiont-mediated cytolysis of host cell viral life cycle disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction viral release from host cell by cytolysis exit from host cell viral process cytolysis in another organism viral release from host cell disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation apoptotic process cell death programmed cell death membrane organization cellular component organization myelination myelin maintenance axon ensheathment ensheathment of neurons plasma membrane organization cellular component organization or biogenesis endomembrane system organization cell chemotaxis cellular response to stimulus chemotaxis dendritic cell chemotaxis leukocyte migration dendritic cell migration cellular response to chemical stimulus taxis immune system process response to chemical mononuclear cell migration cell migration cell motility leukocyte chemotaxis locomotion response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus positive regulation of cytosolic calcium ion concentration regulation of biological quality neurogenesis cellular developmental process cell differentiation regulation of response to external stimulus regulation of chemotaxis regulation of response to stimulus regulation of locomotion immune response cell surface receptor signaling pathway chemokine (C-X-C motif) ligand 12 signaling pathway signaling CXCL12-activated CXCR4 signaling pathway response to cytokine response to chemokine cytokine-mediated signaling pathway cellular response to chemokine chemokine-mediated signaling pathway cell communication response to peptide G protein-coupled receptor signaling pathway cellular response to cytokine stimulus signal transduction C-X-C chemokine receptor CXCR4 signaling pathway intracellular signal transduction calcium-mediated signaling intracellular signaling cassette regulation of multicellular organismal development regulation of developmental process positive regulation of biological process vasculature development regulation of vasculature development circulatory system development positive regulation of developmental process positive regulation of vasculature development positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of macrophage migration inhibitory factor signaling pathway positive regulation of response to cytokine stimulus positive regulation of response to stimulus macrophage migration inhibitory factor signaling pathway positive regulation of cellular process regulation of signaling regulation of macrophage migration inhibitory factor signaling pathway regulation of cytokine-mediated signaling pathway regulation of response to cytokine stimulus regulation of cell communication positive regulation of cytokine-mediated signaling pathway positive regulation of signaling homeostatic process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis regulation of metabolic process positive regulation of locomotion regulation of cell motility positive regulation of cell migration positive regulation of cell motility regulation of cell migration response to virus inflammatory response positive regulation of nervous system development cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development gliogenesis positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of oligodendrocyte differentiation positive regulation of cell development regulation of glial cell differentiation positive regulation of glial cell differentiation oligodendrocyte differentiation glial cell differentiation regulation of oligodendrocyte differentiation	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell leading edge intracellular anatomical structure cytoplasm anchoring junction cell junction intracellular organelle lytic vacuole vacuole intracellular membrane-bounded organelle lysosome protein-containing complex cytoplasmic vesicle intracellular vesicle early endosome endosome endomembrane system late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR001811	Chemokine interleukin-8-like domain	Domain
B [auth C]	IPR039809	Chemokine beta/gamma/delta	Family
B [auth C]	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
B [auth C]	IPR000827	CC chemokine, conserved site	Conserved Site
A	IPR052619	Bacteriophage lysozyme-like	Family
A	IPR001165	T4-type lysozyme	Family
A	IPR034690	Endolysin T4 type	Family
A	IPR002196	Glycoside hydrolase, family 24	Family
A	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
A	IPR000355	Chemokine receptor family	Family
A	IPR022726	CXC chemokine receptor 4 N-terminal domain	Domain
A	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A	IPR001277	CXC chemokine receptor 4/atypical chemokine receptor 2	Family
A	IPR050119	C-C chemokine receptor type 1-9-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P61073	WHIM syndrome juvenile idiopathic arthritis rheumatoid arthritis breast carcinoma Neoplasm Invasiveness breast cancer neuralgia interstitial cystitis juvenile dermatomyositis osteosarcoma lung carcinoma pilocytic astrocytoma lymphoplasmacytic lymphoma primitive neuroectodermal tumor AIDS WHIM syndrome juvenile idiopathic arthritis rheumatoid arthritis breast carcinoma Neoplasm Invasiveness breast cancer neuralgia interstitial cystitis juvenile dermatomyositis osteosarcoma lung carcinoma pilocytic astrocytoma lymphoplasmacytic lymphoma primitive neuroectodermal tumor AIDS malignant mesothelioma Sjogren syndrome atypical teratoid rhabdoid tumor Waldenstrom macroglobulinemia breast disease congenital anemia nephrosclerosis ductal breast carcinoma in situ glioblastoma invasive ductal breast carcinoma ovarian cancer large cell medulloblastoma periodontitis lung disease pituitary cancer malignant ependymoma psoriasis astrocytic tumor tuberculosis cancer cutaneous lupus erythematosus dermatomyositis esophageal adenocarcinoma hematologic disease oligodendroglioma pancreatic ductal adenocarcinoma lung cancer lymphatic system disease plasma cell myeloma malignant glioma atopic eczema malignant pancreatic neoplasm ulcerative colitis medulloblastoma cystic fibrosis Down syndrome gastric carcinoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B [auth C]	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, B [auth C]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B [auth C]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth C]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	CXCR4 chemokine receptor complexed with viral chemokine antagonist vMIP-II

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.