3ODU

The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t

External Resource: Annotation

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
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	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091230	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091230	3000473	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8091230	3000473	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8091230	3000473	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	7tm_1_1	e3oduA1	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	e3oduA2	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Phage_lysozyme_2	ECOD (1.6)
B	7tm_1_1	e3oduB3	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)
B	Phage_lysozyme_2	e3oduB4	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)
A	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
A	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
B	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
B	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
A, B	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	C-X-C chemokine receptor type 4, Lysozyme Chimera	molecular transducer activity coreceptor activity signaling receptor activity cytoskeletal protein binding myosin light chain binding protein binding binding myosin binding small molecule binding C-C chemokine binding chemokine binding cytokine binding G protein-coupled chemoattractant receptor activity C-X-C motif chemokine 12 receptor activity molecular transducer activity coreceptor activity signaling receptor activity cytoskeletal protein binding myosin light chain binding protein binding binding myosin binding small molecule 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 hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity	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 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 cellular process neuron recognition cellular developmental process cell development generation of neurons neurogenesis neuron differentiation cell differentiation neuron development cell recognition regulation of calcium ion transport regulation of localization transport regulation of transport regulation of monoatomic ion transport establishment of localization metal ion transport calcium ion transport localization monoatomic ion transport regulation of metal ion transport monoatomic cation transport response to stimulus response to mechanical stimulus response to abiotic stimulus response to external stimulus response to ultrasound chemotaxis positive regulation of locomotion regulation of response to external stimulus positive regulation of biological process regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus taxis regulation of response to stimulus response to chemical regulation of locomotion locomotion forebrain development telencephalon cell migration forebrain cell migration cell migration telencephalon development cell motility apoptotic process cell death programmed cell death epithelium development endothelium development tube development morphogenesis of an endothelium endothelial tube morphogenesis morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis tube morphogenesis epithelial tube morphogenesis regulation of viral process viral process 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 dendritic cell chemotaxis leukocyte migration dendritic cell migration cellular response to chemical stimulus immune system process mononuclear cell migration leukocyte chemotaxis detection of external stimulus system process detection of stimulus involved in sensory perception of pain nervous system process sensory perception of temperature stimulus sensory perception of pain detection of temperature stimulus involved in sensory perception response to temperature stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of temperature stimulus detection of stimulus involved in sensory perception detection of temperature stimulus involved in sensory perception of pain response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels cellular response to xenobiotic stimulus response to xenobiotic stimulus epithelial cell development epithelial cell differentiation regulation of growth developmental growth cell projection organization neuron projection development regulation of cell morphogenesis positive regulation of developmental process cell projection morphogenesis neuron projection morphogenesis positive regulation of developmental growth developmental growth involved in morphogenesis positive regulation of dendrite extension regulation of cellular component organization regulation of developmental process plasma membrane bounded cell projection morphogenesis cell growth cell morphogenesis dendrite extension positive regulation of cellular process regulation of anatomical structure morphogenesis neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth regulation of dendrite extension positive regulation of cell growth regulation of cell growth positive regulation of growth positive regulation of cytosolic calcium ion concentration regulation of biological quality detection of mechanical stimulus involved in sensory perception of pain detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of mechanical stimulus 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 response to activity regulation of cell motility positive regulation of mesenchymal stem cell migration positive regulation of cell migration regulation of mesenchymal stem cell migration mesenchymal stem cell migration positive regulation of cell motility regulation of cell migration intracellular signal transduction calcium-mediated signaling intracellular signaling cassette endothelial cell differentiation angiogenesis regulation of vasculature development regulation of response to wounding positive regulation of vascular wound healing vascular wound healing regulation of response to stress regulation of multicellular organismal process response to wounding blood vessel development positive regulation of response to wounding wound healing regulation of multicellular organismal development blood vessel morphogenesis angiogenesis involved in wound healing positive regulation of angiogenesis vasculature development circulatory system development positive regulation of vasculature development positive regulation of wound healing regulation of angiogenesis regulation of wound healing anatomical structure formation involved in morphogenesis positive regulation of multicellular organismal process regulation of vascular wound healing 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 macrophage migration inhibitory factor signaling pathway 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 metabolic process regulation of metabolic process regulation of programmed cell death response to tacrolimus response to oxygen-containing compound response to nitrogen compound response to organic cyclic compound heart process circulatory system process cardiac muscle contraction heart contraction muscle contraction muscle system process blood circulation striated muscle contraction biological process involved in interspecies interaction between organisms response to other organism response to external biotic stimulus response to virus response to biotic stimulus defense response inflammatory response neuron migration positive regulation of nervous system development regulation of cell differentiation regulation of neurogenesis 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 regulation of glial cell differentiation positive regulation of cell development positive regulation of glial cell differentiation oligodendrocyte differentiation glial cell differentiation regulation of oligodendrocyte differentiation defense response to bacterium defense response to other organism response to bacterium 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 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 disruption of cellular anatomical structure in another organism exit from host cell 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 disruption of plasma membrane integrity in another organism cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process	cell periphery cellular anatomical structure 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 cell periphery cellular anatomical structure 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 host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000355	Chemokine receptor family	Family
A, B	IPR022726	CXC chemokine receptor 4 N-terminal domain	Domain
A, B	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, B	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A, B	IPR001277	CXC chemokine receptor 4/atypical chemokine receptor 2	Family
A, B	IPR050119	C-C chemokine receptor type 1-9-like	Family
A, B	IPR052619	Bacteriophage lysozyme-like	Family
A, B	IPR001165	T4-type lysozyme	Family
A, B	IPR034690	Endolysin T4 type	Family
A, B	IPR002196	Glycoside hydrolase, family 24	Family
A, B	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A, B	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	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 breast disease Waldenstrom macroglobulinemia 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	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	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	CXCR4 chemokine receptor complexed with IT1t antagonist

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.