5DNF | pdb_00005dnf

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)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
G	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)
E	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)
C	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)
A	Asp_Arg_Hydrox	e5dnfA1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (develop294)
B	Asp_Arg_Hydrox	e5dnfB1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (develop294)
H	Asp_Arg_Hydrox	e5dnfH1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (develop294)
I	Asp_Arg_Hydrox	e5dnfI1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (develop294)
G	Asp_Arg_Hydrox	e5dnfG1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (develop294)
F	Asp_Arg_Hydrox	e5dnfF1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (develop294)
E	Asp_Arg_Hydrox	e5dnfE1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (develop294)
D	Asp_Arg_Hydrox	e5dnfD1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (develop294)
C	Asp_Arg_Hydrox	e5dnfC1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
G	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)
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)

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 phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity glycerophospholipase activity hydrolase activity C-type glycerophospholipase activity phosphatidylinositol-4,5-bisphosphate phospholipase C 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 cell communication regulation of biological process regulation of signaling regulation of cellular process positive regulation of signal transduction response to stimulus signaling biological regulation positive regulation of biological process regulation of signal transduction positive regulation of G protein-coupled receptor signaling pathway cell communication positive regulation of response to stimulus regulation of response to stimulus cellular response to stimulus positive regulation of cell communication regulation of biological process regulation of signaling regulation of cellular process positive regulation of signal transduction response to stimulus signaling biological regulation positive regulation of biological process regulation of signal transduction positive regulation of G protein-coupled receptor signaling pathway cell communication positive regulation of response to stimulus regulation of response to stimulus regulation of cell communication G protein-coupled receptor signaling pathway cellular process signal transduction regulation of G protein-coupled receptor signaling pathway positive regulation of cellular process positive regulation of signaling phospholipase D-activating G protein-coupled receptor signaling pathway positive regulation of locomotion regulation of cell motility 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 leukocyte chemotaxis positive regulation of lymphocyte migration regulation of leukocyte migration lymphocyte migration response to external stimulus positive regulation of leukocyte chemotaxis leukocyte migration response to chemical regulation of locomotion regulation of natural killer cell chemotaxis regulation of response to external stimulus lymphocyte chemotaxis regulation of lymphocyte migration positive regulation of lymphocyte chemotaxis 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 cell chemotaxis positive regulation of leukocyte migration regulation of chemotaxis cellular response to chemical stimulus immune system process mononuclear cell migration leukocyte chemotaxis cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway intracellular signal transduction regulation of intracellular signal transduction positive regulation of TOR signaling TOR signaling regulation of TOR signaling positive regulation of intracellular signal transduction cell-cell signaling 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 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 granulocyte migration macrophage chemotaxis regulation of granulocyte chemotaxis regulation of macrophage migration myeloid leukocyte migration regulation of macrophage chemotaxis granulocyte chemotaxis positive regulation of macrophage chemotaxis regulation of localization establishment of protein localization nitrogen compound transport regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport hormone secretion protein localization to extracellular region localization peptide secretion regulation of secretion by cell secretion by cell signal release intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of transport secretion regulation of hormone levels regulation of peptide transport regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion establishment of localization regulation of protein secretion regulation of secretion peptide transport protein transport 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 life cycle regulation of viral process 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 biological process involved in interspecies interaction between organisms host-mediated suppression of viral proces host-mediated perturbation of viral transcription host-mediated suppression of viral transcription host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont 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 positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process translational initiation protein metabolic process regulation of biosynthetic process regulation of translational initiation regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process metabolic process positive regulation of translational initiation macromolecule metabolic process regulation of metabolic process 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 peptide cellular response to interleukin-1 response to cytokine cellular response to cytokine stimulus 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 positive regulation of receptor signaling pathway via STAT regulation of receptor signaling pathway via STAT 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 positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction intracellular signaling cassette 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 immune response response to other organism response to type II interferon defense response to symbiont cellular response to type II interferon response to biotic stimulus defense response to other organism innate immune response response to external biotic stimulus humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide 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 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 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 positive regulation of neuroinflammatory response positive regulation of inflammatory response regulation of neuroinflammatory response neuroinflammatory response cellular response to virus chemokine (C-C motif) ligand 5 signaling pathway	cellular anatomical structure membrane intracellular anatomical structure cytoplasm 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 subependymal giant cell astrocytoma hematologic disease interstitial cystitis acute myeloid leukemia arthritic joint disease lung carcinoma atypical teratoid rhabdoid tumor malignant mesothelioma glomerulonephritis asthma primary biliary cholangitis autoimmune hepatitis pulmonary fibrosis Liver Cirrhosis, Experimental glioblastoma subependymal giant cell astrocytoma hematologic disease interstitial cystitis acute myeloid leukemia arthritic joint disease lung carcinoma atypical teratoid rhabdoid tumor cancer peripheral neuropathy cutaneous lupus erythematosus primitive neuroectodermal tumor sarcoidosis idiopathic interstitial pneumonia invasive ductal breast carcinoma alcoholic hepatitis lung adenocarcinoma 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 allergic disease lung cancer atopic eczema malignant glioma nasopharyngeal carcinoma ovarian cancer peripheral nervous system disease Crohn disease primary hyperoxaluria dermatitis, atopic

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.