4R9Y | pdb_00004r9y

Crystal structure of KKOFab in complex with platelet factor 4

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2B Superfamily	Interleukin 8-like chemokines	8035720	3001955	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Interleukin 8-like chemokines	8035720	3001955	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Interleukin 8-like chemokines	8035720	3001955	SCOP2B (2022-06-29)
F [auth A]	SCOP2B Superfamily	Interleukin 8-like chemokines	8035720	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 [auth D]	IL8_1	e4r9yD1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: IL8_1	ECOD (1.6)
B [auth C]	IL8_1	e4r9yC1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: IL8_1	ECOD (1.6)
E [auth B]	IL8_1	e4r9yB1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: IL8_1	ECOD (1.6)
F [auth A]	IL8_1	e4r9yA1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: IL8_1	ECOD (1.6)
C [auth L]	C1-set_4	e4r9yL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
C [auth L]	V-set	e4r9yL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
G [auth M]	C1-set_4	e4r9yM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
G [auth M]	V-set	e4r9yM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
D [auth H]	V-set_8	e4r9yH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D [auth H]	C1-set_1	e4r9yH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
H [auth N]	V-set_8	e4r9yN2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
H [auth N]	C1-set_1	e4r9yN3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C [auth L], G [auth M]	Platelet factor 4 antibody KKO	L-KAPPA	Mus musculus (house mouse)	IGKV6-1501, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2B_KAPPA	IMGT (202510-0)
D [auth H], H [auth N]	Platelet factor 4 antibody KKO	VH-CH1	Mus musculus (house mouse)	IGHV1S8102, IGHJ301, IGHG2B*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2B_KAPPA	IMGT (202510-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L], G [auth M]	Light Chain	IGKV6	Kappa	platelet factor 4 \| platelet factor 4	SAbDab (2025-03-21)
D [auth H], H [auth N]	Heavy Chain	IGHV1	-	platelet factor 4 \| platelet factor 4	SAbDab (2025-03-21)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth C], E [auth B], F [auth A]	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 [auth D], B [auth C], E [auth B], F [auth A]	Platelet factor 4	molecular transducer activity binding molecular function activator activity signaling receptor binding signaling receptor activity G protein-coupled receptor binding signaling receptor activator activity protein binding cytokine receptor binding chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity chemokine receptor binding molecular transducer activity binding molecular function activator activity signaling receptor binding signaling receptor activity G protein-coupled receptor binding signaling receptor activator activity protein binding cytokine receptor binding chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity chemokine receptor binding receptor ligand activity CXCR chemokine receptor binding CXCR3 chemokine receptor binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus signal transduction negative regulation of extrinsic apoptotic signaling pathway in absence of ligand signal transduction in absence of ligand negative regulation of signaling negative regulation of biological process regulation of signal transduction regulation of programmed cell death negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cell chemotaxis chemotaxis neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion response to chemokine cellular response to chemokine chemokine-mediated signaling pathway G protein-coupled receptor signaling pathway biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin multicellular organismal process regulation of body fluid levels regulation of response to external stimulus regulation of response to wounding regulation of coagulation response to stress regulation of response to stress coagulation regulation of multicellular organismal process regulation of biological quality response to wounding regulation of hemostasis wound healing negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation hemostasis negative regulation of response to wounding blood coagulation negative regulation of hemostasis negative regulation of coagulation negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process negative regulation of metabolic process regulation of MHC class II biosynthetic process negative regulation of MHC class II biosynthetic process MHC class II biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process developmental process regulation of developmental process cellular developmental process macrophage derived foam cell differentiation regulation of cell differentiation positive regulation of developmental process foam cell differentiation positive regulation of cell differentiation cell differentiation regulation of macrophage derived foam cell differentiation positive regulation of macrophage derived foam cell differentiation regulation of megakaryocyte differentiation cell development megakaryocyte differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation negative regulation of myeloid cell differentiation myeloid cell differentiation regulation of hemopoiesis adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway cell activation platelet activation defense response defense response to protozoan response to protozoan defense response to other organism defense response to symbiont disruption of cell in another organism biological process involved in symbiotic interaction killing by host of symbiont cells disruption of anatomical structure in another organism biological process involved in interaction with symbiont killing of cells of another organism cell killing monocyte chemotaxis mononuclear cell migration humoral immune response immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide cell population proliferation regulation of cell population proliferation myeloid leukocyte differentiation regulation of leukocyte differentiation mononuclear cell differentiation positive regulation of hemopoiesis regulation of macrophage differentiation positive regulation of immune system process positive regulation of cell development macrophage differentiation regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation positive regulation of macrophage differentiation positive regulation of myeloid cell differentiation positive regulation of multicellular organismal process positive regulation of leukocyte differentiation leukocyte differentiation inflammatory response angiogenesis regulation of vasculature development tube morphogenesis regulation of anatomical structure morphogenesis system development blood vessel development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production cytokine production regulation of cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production positive regulation of cytokine production positive regulation of DNA-templated transcription RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription	cell periphery extracellular matrix cellular anatomical structure external encapsulating structure collagen-containing extracellular matrix intracellular anatomical structure cytoplasm extracellular region membrane-bounded organelle vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle cell periphery extracellular matrix cellular anatomical structure external encapsulating structure collagen-containing extracellular matrix intracellular anatomical structure cytoplasm extracellular region membrane-bounded organelle vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen organelle secretory granule secretory vesicle platelet alpha granule vesicle platelet alpha granule lumen extracellular space
C [auth L], G [auth M]	Platelet factor 4 antibody KKO light chain	-	-	-
D [auth H], H [auth N]	Platelet factor 4 antibody KKO heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth C], E [auth B], F [auth A]	IPR001811	Chemokine interleukin-8-like domain	Domain
A [auth D], B [auth C], E [auth B], F [auth A]	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
A [auth D], B [auth C], E [auth B], F [auth A]	IPR001089	CXC chemokine	Family
A [auth D], B [auth C], E [auth B], F [auth A]	IPR039809	Chemokine beta/gamma/delta	Family
A [auth D], B [auth C], E [auth B], F [auth A]	IPR033899	CXC Chemokine domain	Domain
A [auth D], B [auth C], E [auth B], F [auth A]	IPR018048	CXC chemokine, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D], B [auth C], E [auth B], F [auth A]	Pharos: P02776	thrombocytopenia allergic disease pneumonia autoimmune disease thrombotic disease Thrombus hepatocellular carcinoma MALT lymphoma ulcerative colitis gastric cancer malignant mesothelioma non-small cell lung carcinoma pneumonitis exocrine pancreatic carcinoma gastric carcinoma thrombocytopenia allergic disease pneumonia autoimmune disease thrombotic disease Thrombus hepatocellular carcinoma MALT lymphoma ulcerative colitis gastric cancer malignant mesothelioma non-small cell lung carcinoma pneumonitis exocrine pancreatic carcinoma gastric carcinoma inflammatory bowel disease malignant pancreatic neoplasm osteosarcoma

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.