3OE6

Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in I222 spacegroup

Present annotations:

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Product Annotation
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	G protein-coupled receptor-like	8091230	3000473	SCOP2B (2022-06-29)
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)

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	e3oe6A3	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	e3oe6A4	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 (4.2.0)
A	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Identifier	Description	Comments	Source
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)	-	Family
A	PF12109	CXCR4 Chemokine receptor N terminal (CXCR4_N)	CXCR4 Chemokine receptor N terminal	CXCR4 and its ligand stromal cell-derived factor-1 (a.k.a. CXCL12) are essential for proper fetal development. CXCR4 is also the major coreceptor for T-tropic strains of human immunodeficiency virus 1 (HIV-1), and SDF-1 inhibits HIV-1 infection. Addi ...	CXCR4 and its ligand stromal cell-derived factor-1 (a.k.a. CXCL12) are essential for proper fetal development. CXCR4 is also the major coreceptor for T-tropic strains of human immunodeficiency virus 1 (HIV-1), and SDF-1 inhibits HIV-1 infection. Additionally, SDF-1 and CXCR4 mediate cancer cell migration and metastasis. The N terminal domain of most chemokine receptors is the ligand binding domain and so the N terminal domain of CXCR4 is the binding site for SDF-1. [1]	Domain

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	C-X-C chemokine receptor type 4, Lysozyme Chimera	actin binding binding protein binding cytoskeletal protein binding cytokine binding chemokine binding C-C chemokine binding coreceptor activity signaling receptor activity molecular transducer activity transmembrane signaling receptor activity G protein-coupled receptor activity myosin binding myosin light chain binding small molecule binding ubiquitin-like protein binding ubiquitin binding enzyme binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding lysozyme activity catalytic activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity	cellular process response to organic substance response to cytokine response to chemical response to stimulus cellular response to stimulus cellular response to chemical stimulus cellular response to organic substance cellular response to cytokine stimulus response to xenobiotic stimulus cellular response to xenobiotic stimulus cell migration regulation of cell migration positive regulation of cell migration locomotion regulation of locomotion positive regulation of locomotion positive regulation of biological process positive regulation of cellular process cell motility regulation of biological process regulation of cellular process biological regulation mesenchymal stem cell migration regulation of mesenchymal stem cell migration positive regulation of mesenchymal stem cell migration regulation of cell motility positive regulation of cell motility cell death programmed cell death regulation of programmed cell death viral process regulation of viral process response to activity response to organonitrogen compound response to organic cyclic compound response to isoquinoline alkaloid response to morphine response to alkaloid response to nitrogen compound response to salt response to external stimulus response to mechanical stimulus response to abiotic stimulus response to ultrasound response to biotic stimulus response to virus response to external biotic stimulus biological process involved in interspecies interaction between organisms response to other organism metabolic process catabolic process macromolecule catabolic process cell wall macromolecule catabolic process macromolecule metabolic process cell wall macromolecule metabolic process cell wall organization or biogenesis organic substance metabolic process organic substance catabolic process cytolysis	cell junction anchoring junction cellular anatomical entity cell leading edge cell surface intracellular anatomical structure cytoplasm cytoplasmic vesicle vesicle organelle membrane-bounded organelle intracellular organelle intracellular membrane-bounded organelle intracellular vesicle endosome early endosome endomembrane system plasma membrane external side of plasma membrane membrane cell periphery side of membrane extracellular region extracellular space extracellular organelle extracellular membrane-bounded organelle extracellular exosome extracellular vesicle late endosome nucleus protein-containing complex host cellular component host cell cytoplasm host cell part host intracellular part host intracellular region host cell

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	CXCR4 chemokine receptor complexed with IT1t antagonist

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.