5DNF

Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin

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)
E	d5dnfe_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	RANTES (regulated upon activation, normal T-cell expressed and secreted)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d5dnff_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	RANTES (regulated upon activation, normal T-cell expressed and secreted)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5dnfg_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	RANTES (regulated upon activation, normal T-cell expressed and secreted)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5dnfa_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	RANTES (regulated upon activation, normal T-cell expressed and secreted)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5dnfb_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	RANTES (regulated upon activation, normal T-cell expressed and secreted)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5dnfc_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	RANTES (regulated upon activation, normal T-cell expressed and secreted)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5dnfd_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	RANTES (regulated upon activation, normal T-cell expressed and secreted)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d5dnfh_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	RANTES (regulated upon activation, normal T-cell expressed and secreted)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d5dnfi_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	RANTES (regulated upon activation, normal T-cell expressed and secreted)	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)
E	SCOP2B Superfamily	Interleukin 8-like chemokines	8034294	3001955	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Interleukin 8-like chemokines	8034294	3001955	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Interleukin 8-like chemokines	8034294	3001955	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Interleukin 8-like chemokines	8034294	3001955	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Interleukin 8-like chemokines	8034294	3001955	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Interleukin 8-like chemokines	8034294	3001955	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Interleukin 8-like chemokines	8034294	3001955	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Interleukin 8-like chemokines	8034294	3001955	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Interleukin 8-like chemokines	8034294	3001955	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)
E	PF00048	e5dnfE1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)
F	PF00048	e5dnfF1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)
G	PF00048	e5dnfG1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)
A	PF00048	e5dnfA1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)
B	PF00048	e5dnfB1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)
C	PF00048	e5dnfC1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)
D	PF00048	e5dnfD1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)
H	PF00048	e5dnfH1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)
I	PF00048	e5dnfI1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
F	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
G	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)
B	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)
D	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
H	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
I	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, G, H, I	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, G, H, I	C-C motif chemokine 5	CCR5 chemokine receptor binding CCR chemokine receptor binding protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding protein tyrosine kinase activator activity enzyme regulator activity kinase activator activity enzyme activator activity receptor signaling protein tyrosine kinase activator activity molecular function activator activity CCR5 chemokine receptor binding CCR chemokine receptor binding protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding protein tyrosine kinase activator activity enzyme regulator activity kinase activator activity enzyme activator activity receptor signaling protein tyrosine kinase activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups identical protein binding signaling receptor activator activity chemokine activity cytokine activity signaling receptor regulator activity receptor ligand activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity phospholipase C activity hydrolase activity phosphatidylinositol phospholipase C activity phospholipase activity lipase activity CCR4 chemokine receptor binding CCR1 chemokine receptor binding protein homodimerization activity protein dimerization activity chemoattractant activity phospholipase activator activity lipase activator activity molecular function inhibitor activity signaling receptor inhibitor activity chemokine receptor antagonist activity receptor antagonist activity	cellular response to stimulus positive regulation of locomotion regulation of cell motility regulation of cellular process response to stimulus positive regulation of chemotaxis positive regulation of cell migration regulation of lymphocyte chemotaxis natural killer cell chemotaxis taxis positive regulation of natural killer cell chemotaxis cell migration regulation of immune system process regulation of mononuclear cell migration cellular response to stimulus positive regulation of locomotion regulation of cell motility regulation of cellular process response to stimulus positive regulation of chemotaxis positive regulation of cell migration regulation of lymphocyte chemotaxis natural killer cell chemotaxis taxis positive regulation of natural killer cell chemotaxis cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process chemotaxis regulation of biological process regulation of leukocyte chemotaxis positive regulation of lymphocyte migration regulation of leukocyte migration lymphocyte migration response to external stimulus positive regulation of leukocyte chemotaxis leukocyte migration regulation of response to stimulus response to chemical regulation of locomotion regulation of natural killer cell chemotaxis regulation of response to external stimulus positive regulation of biological process lymphocyte chemotaxis regulation of lymphocyte migration positive regulation of lymphocyte chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration positive regulation of mononuclear cell migration cell motility locomotion positive regulation of cellular process cell chemotaxis biological regulation positive regulation of leukocyte migration regulation of chemotaxis cellular response to chemical stimulus immune system process mononuclear cell migration cellular process leukocyte chemotaxis neutrophil chemotaxis neutrophil migration granulocyte migration granulocyte chemotaxis myeloid leukocyte migration signaling cell-cell signaling cell communication inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis response to toxic substance positive regulation of cell communication positive regulation of signal transduction positive regulation of phosphorylation regulation of catalytic activity positive regulation of receptor signaling pathway via STAT regulation of signal transduction regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process regulation of receptor signaling pathway via JAK-STAT positive regulation of macromolecule metabolic process signal transduction protein modification process phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process primary metabolic process regulation of cellular metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification positive regulation of activation of Janus kinase activity metabolic process regulation of phosphorus metabolic process macromolecule metabolic process regulation of receptor signaling pathway via STAT regulation of metabolic process cell surface receptor signaling pathway via STAT regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process peptidyl-tyrosine modification positive regulation of receptor signaling pathway via JAK-STAT regulation of activation of Janus kinase activity positive regulation of molecular function positive regulation of protein modification process positive regulation of peptidyl-tyrosine phosphorylation organic substance metabolic process protein metabolic process positive regulation of protein kinase activity activation of Janus kinase activity regulation of signaling organonitrogen compound metabolic process positive regulation of transferase activity cell surface receptor signaling pathway regulation of peptidyl-tyrosine phosphorylation positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of cell communication regulation of phosphorylation peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT positive regulation of signaling positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration smooth muscle cell migration muscle cell migration response to fibroblast growth factor cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor cellular response to fibroblast growth factor stimulus macrophage migration positive regulation of macrophage migration macrophage chemotaxis regulation of granulocyte chemotaxis regulation of macrophage migration regulation of macrophage chemotaxis positive regulation of macrophage chemotaxis protein localization regulation of localization establishment of protein localization nitrogen compound transport localization cellular macromolecule localization regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels organic substance transport establishment of protein localization to extracellular region protein secretion establishment of localization regulation of protein secretion regulation of secretion cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport hormone secretion protein localization to extracellular region peptide secretion secretion by cell regulation of secretion by cell amide transport signal release secretion regulation of transport regulation of peptide transport regulation of establishment of protein localization export from cell regulation of protein transport peptide transport protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion dendritic cell chemotaxis dendritic cell migration multicellular organismal process regulation of leukocyte activation cell activation regulation of cell activation regulation of T cell activation lymphocyte activation leukocyte activation T cell activation regulation of multicellular organismal process regulation of lymphocyte activation positive regulation of monocyte chemotaxis regulation of monocyte chemotaxis monocyte chemotaxis positive regulation of viral genome replication positive regulation of viral process viral life cycle regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication regulation of calcium ion transport positive regulation of calcium ion transport regulation of monoatomic ion transport calcium ion transport metal ion transport positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport positive regulation of T cell migration regulation of T cell migration T cell migration cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation cell adhesion cell-cell adhesion leukocyte cell-cell adhesion eosinophil chemotaxis eosinophil migration regulation of homotypic cell-cell adhesion positive regulation of cell adhesion regulation of cell adhesion homotypic cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of homotypic cell-cell adhesion regulation of cell-cell adhesion regulation of biosynthetic process cellular biosynthetic process regulation of cellular biosynthetic process biosynthetic process positive regulation of biosynthetic process positive regulation of cellular biosynthetic process regulation of leukocyte apoptotic process regulation of lymphocyte 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 T cell apoptotic process lymphocyte apoptotic process negative regulation of apoptotic process negative regulation of leukocyte apoptotic process negative regulation of cellular process regulation of T cell apoptotic process T cell apoptotic process apoptotic process programmed cell death negative regulation of lymphocyte apoptotic process organonitrogen compound biosynthetic process positive regulation of translation positive regulation of macromolecule biosynthetic process post-transcriptional regulation of gene expression organic substance biosynthetic process translational initiation regulation of translational initiation gene expression translation macromolecule biosynthetic process regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process positive regulation of translational initiation positive regulation of programmed cell death positive regulation of lymphocyte apoptotic process positive regulation of apoptotic process positive regulation of T cell apoptotic process positive regulation of leukocyte apoptotic process positive regulation of cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of multicellular organismal process positive regulation of leukocyte cell-cell adhesion leukocyte proliferation positive regulation of lymphocyte activation positive regulation of mononuclear cell proliferation T cell proliferation regulation of lymphocyte proliferation regulation of T cell proliferation regulation of mononuclear cell proliferation response to organic substance response to cytokine cellular response to interleukin-1 cellular response to cytokine stimulus cellular response to organic substance response to interleukin-1 macrophage apoptotic process myeloid cell apoptotic process negative regulation of macrophage apoptotic process regulation of macrophage apoptotic process inflammatory cell apoptotic process negative regulation of myeloid cell apoptotic process regulation of myeloid cell apoptotic process viral gene expression biological process involved in interspecies interaction between organisms negative regulation by host of viral transcription modulation by host of symbiont process biological process involved in interaction with symbiont viral transcription biological process involved in symbiotic interaction intracellular signal transduction positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade cell-cell adhesion mediated by integrin positive regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell-cell adhesion mediated by integrin positive regulation of cell-cell adhesion mediated by integrin cell adhesion mediated by integrin neutrophil activation myeloid leukocyte activation granulocyte activation response to chemokine cytokine-mediated signaling pathway cellular response to chemokine chemokine-mediated signaling pathway G protein-coupled receptor signaling pathway positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation 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 regulation of defense response regulation of chronic inflammatory response chronic inflammatory response defense response regulation of inflammatory response response to stress regulation of response to stress inflammatory response cellular response to tumor necrosis factor response to tumor necrosis factor response to type II interferon cellular response to type II interferon response to biotic stimulus innate immune response response to external biotic stimulus immune response response to other organism defense response to symbiont defense response to other organism tyrosine phosphorylation of STAT protein regulation of tyrosine phosphorylation of STAT protein positive regulation of tyrosine phosphorylation of STAT protein negative regulation of viral genome replication negative regulation of viral process response to virus positive regulation of T cell chemotaxis regulation of T cell chemotaxis T cell chemotaxis regulation of phospholipase activity positive regulation of phospholipase activity activation of phospholipase D activity positive regulation of lipase activity positive regulation of hydrolase activity regulation of hydrolase activity regulation of lipase activity negative regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction negative regulation of G protein-coupled receptor signaling pathway negative regulation of cell communication regulation of G protein-coupled receptor signaling pathway exocytosis vesicle-mediated transport positive regulation of response to biotic stimulus regulation of response to biotic stimulus positive regulation of immune response positive regulation of innate immune response regulation of innate immune response positive regulation of defense response regulation of immune response cellular response to virus	intracellular anatomical structure cytoplasm cellular anatomical entity extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR001811	Chemokine interleukin-8-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR000827	CC chemokine, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR039809	Chemokine beta/gamma/delta	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I	Pharos: P13501	malignant mesothelioma glomerulonephritis asthma primary biliary cholangitis autoimmune hepatitis pulmonary fibrosis Liver Cirrhosis, Experimental glioblastoma hematologic disease subependymal giant cell astrocytoma interstitial cystitis acute myeloid leukemia lung carcinoma arthritic joint disease atypical teratoid rhabdoid tumor malignant mesothelioma glomerulonephritis asthma primary biliary cholangitis autoimmune hepatitis pulmonary fibrosis Liver Cirrhosis, Experimental glioblastoma hematologic disease subependymal giant cell astrocytoma interstitial cystitis acute myeloid leukemia lung carcinoma arthritic joint disease atypical teratoid rhabdoid tumor cancer cutaneous lupus erythematosus peripheral neuropathy primitive neuroectodermal tumor sarcoidosis idiopathic interstitial pneumonia invasive ductal breast carcinoma lung adenocarcinoma alcoholic hepatitis malignant ependymoma MALT lymphoma autoimmune disease non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma cystic fibrosis psoriasis Sjogren syndrome HIV infectious disease influenza juvenile dermatomyositis lung cancer allergic disease malignant glioma atopic eczema nasopharyngeal carcinoma ovarian cancer peripheral nervous system disease Crohn disease dermatitis, atopic primary hyperoxaluria

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 R01GM133198.