5EKI | pdb_00005eki

Crystal Structure of Truncated CCL21

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d5ekif_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5ekie_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5ekid_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5ekic_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5ekib_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5ekia_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Interleukin 8-like chemokines	8061445	3001955	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Interleukin 8-like chemokines	8061445	3001955	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Interleukin 8-like chemokines	8061445	3001955	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Interleukin 8-like chemokines	8061445	3001955	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Interleukin 8-like chemokines	8061445	3001955	SCOP2B (2022-06-29)
A	SCOP2 Family	Interleukin 8-like chemokines	8061444	4000912	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Interleukin 8-like chemokines	8061445	3001955	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	PPP2R1A-like_HEAT, VPS15-like_hel	e5ekiF1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (v294.1)
E	PPP2R1A-like_HEAT, VPS15-like_hel	e5ekiE1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (v294.1)
D	PPP2R1A-like_HEAT, VPS15-like_hel	e5ekiD1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (v294.1)
C	PPP2R1A-like_HEAT, VPS15-like_hel	e5ekiC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (v294.1)
B	PPP2R1A-like_HEAT, VPS15-like_hel	e5ekiB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (v294.1)
A	PPP2R1A-like_HEAT, VPS15-like_hel	e5ekiA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
E	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	C-C motif chemokine 21	CCR chemokine receptor binding protein binding binding signaling receptor binding CCR7 chemokine receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding molecular function activator activity signaling receptor activator activity chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity CCR chemokine receptor binding protein binding binding signaling receptor binding CCR7 chemokine receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding molecular function activator activity signaling receptor activator activity chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity	mesangial cell-matrix adhesion cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process response to peptide response to stimulus response to chemical response to chemokine response to cytokine cellular response to cytokine stimulus cellular response to chemokine regulation of cellular process regulation of cellular component organization mesangial cell-matrix adhesion cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process response to peptide response to stimulus response to chemical response to chemokine response to cytokine cellular response to cytokine stimulus cellular response to chemokine 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 positive regulation of cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion chemotaxis positive regulation of locomotion regulation of response to external stimulus response to external stimulus 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 regulation of locomotion locomotion signaling cell-cell signaling cell communication cellular response to stimulus response to ketone response to prostaglandin response to lipid response to endogenous stimulus response to alcohol cellular response to prostaglandin stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to prostaglandin E stimulus cellular response to chemical stimulus cellular response to alcohol response to hormone cellular response to lipid response to prostaglandin E cellular response to ketone cellular response to hormone stimulus positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette signal transduction regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication positive regulation of signaling CCL21-activated CCR7 signaling pathway cell surface receptor signaling pathway chemokine (C-C motif) ligand 21 signaling pathway cytokine-mediated signaling pathway chemokine-mediated signaling pathway G protein-coupled receptor signaling pathway C-C chemokine receptor CCR7 signaling pathway cell chemotaxis dendritic cell chemotaxis leukocyte migration dendritic cell migration immune system process mononuclear cell migration cell migration cell motility leukocyte chemotaxis regulation of localization import into cell transport vesicle-mediated transport localization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of transport endocytosis receptor-mediated endocytosis regulation of cell motility regulation of lymphocyte migration positive regulation of cell migration positive regulation of cell motility regulation of cell migration positive regulation of mononuclear cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process positive regulation of lymphocyte migration regulation of leukocyte migration positive regulation of T cell migration lymphocyte migration positive regulation of leukocyte migration regulation of T cell migration T cell migration ruffle organization eosinophil chemotaxis granulocyte migration eosinophil migration granulocyte chemotaxis myeloid leukocyte migration phospholipase C/protein kinase C signal transduction positive regulation of phospholipase C/protein kinase C signal transduction multicellular organismal process regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of T cell activation cell activation 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 dendritic cell dendrite assembly positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade immune response positive regulation of glycoprotein metabolic process positive regulation of protein metabolic process carbohydrate derivative metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process regulation of glycoprotein biosynthetic process positive regulation of glycoprotein biosynthetic process carbohydrate derivative biosynthetic process regulation of biosynthetic process regulation of protein metabolic process glycoprotein biosynthetic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process macromolecule biosynthetic process regulation of glycoprotein metabolic process biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of locomotion negative regulation of biological process regulation of leukocyte adhesion to vascular endothelial cell negative regulation of cell adhesion leukocyte tethering or rolling negative regulation of leukocyte tethering or rolling negative regulation of cellular extravasation negative regulation of cellular process cellular extravasation negative regulation of cell migration negative regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte tethering or rolling negative regulation of leukocyte migration negative regulation of leukocyte cell-cell adhesion negative regulation of immune system process leukocyte adhesion to vascular endothelial cell negative regulation of cell-cell adhesion negative regulation of cell motility regulation of cellular extravasation positive regulation of neutrophil chemotaxis regulation of leukocyte chemotaxis positive regulation of leukocyte chemotaxis neutrophil 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 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 developmental process cellular developmental process anatomical structure maturation cell differentiation anatomical structure development cell development cell maturation developmental maturation 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 regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of leukocyte apoptotic process regulation of dendritic cell apoptotic process apoptotic process programmed cell death positive regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin cell adhesion mediated by integrin negative regulation of dendritic cell dendrite assembly negative regulation of plasma membrane bounded cell projection assembly negative regulation of cell projection organization regulation of dendritic cell dendrite assembly negative regulation of cellular component organization regulation of myeloid dendritic cell chemotaxis positive regulation of myeloid dendritic cell chemotaxis myeloid dendritic cell chemotaxis positive regulation of dendritic cell chemotaxis regulation of dendritic cell chemotaxis 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 regulation of biological quality 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 humoral immune response biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont antimicrobial humoral response response to biotic stimulus antimicrobial humoral immune response mediated by antimicrobial peptide defense response to other organism response to stress response to external biotic stimulus calcium ion transmembrane import into cytosol monoatomic ion transmembrane transport calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport release of sequestered calcium ion into cytosol intercellular transport monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport immunological synapse formation cell-cell recognition cell recognition filopodium assembly regulation of filopodium assembly positive regulation of filopodium assembly positive regulation of T cell chemotaxis regulation of lymphocyte chemotaxis regulation of T cell chemotaxis lymphocyte chemotaxis positive regulation of lymphocyte chemotaxis T cell chemotaxis establishment of lymphocyte polarity establishment of T cell polarity establishment or maintenance of cell polarity establishment of cell polarity inflammatory response 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	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR001811	Chemokine interleukin-8-like domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR039809	Chemokine beta/gamma/delta	Family
A, B, C, D, E A, B, C, D, E, F	IPR034133	Chemokine CC, DCCL motif-cointaining domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: O00585	rheumatoid arthritis adenoma interstitial cystitis lung cancer breast carcinoma interstitial lung disease lung carcinoma hypertensive disorder lung adenocarcinoma psoriasis

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.