4DN4

Crystal structure of the complex between cnto888 fab and mcp-1 mutant p8a

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-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)
C [auth M]	SCOP2B Superfamily	Interleukin 8-like chemokines	8034307	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 L]	C1-set_4	e4dn4L2	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)
A [auth L]	V-set	e4dn4L1	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)
B [auth H]	V-set_8	e4dn4H4	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)
B [auth H]	C1-set_1	e4dn4H3	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)
C [auth M]	IL8	e4dn4M1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: IL8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth M]	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

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
A [auth L]	CNTO888	L-KAPPA	Homo sapiens (human)	IGKV3-1101, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B [auth H]	CNTO888	VH-CH1	Homo sapiens (human)	IGHV1-6901, IGHV1-6912, IGHV1-6913, IGHV1-69D01, IGHJ101, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV3	Kappa	c-c motif chemokine 2	SAbDab (2024-04-19)
B [auth H]	Heavy Chain	IGHV1	-	c-c motif chemokine 2	SAbDab (2024-04-19)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A [auth L]	Carlumab	CCL2/MCP1	Therapeutic SAbDab (2024-04-19)
B [auth H]	Carlumab	CCL2/MCP1	Therapeutic SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth M]	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 L]	CNTO888 LIGHT CHAIN	-	-	-
B [auth H]	CNTO888 HEAVY CHAIN	-	-	-
C [auth M]	C-C motif chemokine 2	CCR chemokine receptor binding protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding 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 CCR chemokine receptor binding protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding 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 CCR2 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	cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular process cellular response to organic substance signal transduction developmental process multicellular organismal process cellular developmental process glial cell migration nervous system development neurogenesis multicellular organism development gliogenesis cell differentiation anatomical structure development astrocyte cell migration cell migration cell motility system development cell chemotaxis chemotaxis neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration taxis immune system process granulocyte chemotaxis myeloid leukocyte migration leukocyte chemotaxis locomotion helper T cell extravasation T cell extravasation lymphocyte migration mononuclear cell migration cellular extravasation T 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 cellular component organization organelle organization cellular component organization or biogenesis cytoskeleton organization protein phosphorylation organonitrogen compound metabolic process phosphorylation cellular metabolic process primary metabolic process organic substance metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process regulation of calcium ion import regulation of calcium ion transport regulation of localization positive regulation of calcium ion transport positive regulation of calcium ion import transport regulation of transport regulation of monoatomic ion transport positive regulation of biological process establishment of localization calcium ion transport metal ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport calcium ion import monoatomic cation transport regulation of metal ion transport cell adhesion negative regulation of cell population proliferation cell population proliferation endothelial cell proliferation negative regulation of biological process regulation of vascular endothelial cell proliferation negative regulation of endothelial cell proliferation negative regulation of vascular endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation negative regulation of cellular process vascular endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation eosinophil chemotaxis eosinophil migration regulation of glial cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of glial cell apoptotic process cell death glial cell apoptotic process negative regulation of apoptotic process apoptotic process programmed cell death lymphocyte chemotaxis cellular response to interleukin-1 response to interleukin-1 G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger G protein-coupled receptor signaling pathway cellular homeostasis homeostatic process negative regulation of mononuclear cell migration negative regulation of locomotion regulation of cell motility negative regulation of chemotaxis regulation of lymphocyte chemotaxis natural killer cell chemotaxis regulation of immune system process negative regulation of lymphocyte migration regulation of mononuclear cell migration negative regulation of cell migration regulation of leukocyte chemotaxis regulation of leukocyte migration negative regulation of leukocyte migration regulation of response to stimulus regulation of locomotion negative regulation of response to external stimulus negative regulation of cell motility negative regulation of leukocyte chemotaxis regulation of natural killer cell chemotaxis regulation of response to external stimulus regulation of lymphocyte migration regulation of cell migration negative regulation of lymphocyte chemotaxis negative regulation of response to stimulus regulation of chemotaxis negative regulation of immune system process negative regulation of natural killer cell chemotaxis anatomical structure morphogenesis animal organ development animal organ morphogenesis positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development humoral immune response immune response modulation of chemical synaptic transmission synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic synaptic signaling trans-synaptic signaling positive regulation of synaptic transmission cell-cell signaling positive regulation of synaptic transmission, glutamatergic chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling viral genome replication viral process viral life cycle response to chemokine cellular response to chemokine chemokine-mediated 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 neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of nitric-oxide synthase biosynthetic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process nitric-oxide synthase biosynthetic process regulation of biosynthetic process regulation of cellular metabolic process regulation of macromolecule metabolic process macromolecule biosynthetic process regulation of cellular biosynthetic process biosynthetic process regulation of macromolecule biosynthetic process positive regulation of nitric-oxide synthase biosynthetic process regulation of metabolic process positive regulation of cellular biosynthetic process regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis cellular response to tumor necrosis factor response to tumor necrosis factor response to type II interferon cellular response to type II interferon response to stress innate immune response defense response defense response to symbiont defense response to other organism monocyte chemotaxis regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition negative regulation of cell cycle process regulation of mitotic cell cycle phase transition mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle mitotic cell cycle phase transition positive regulation of NMDA glutamate receptor activity regulation of signaling receptor activity monoatomic ion transmembrane transport regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport regulation of transporter activity positive regulation of molecular function positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport regulation of NMDA receptor activity regulation of monoatomic ion transmembrane transporter activity positive regulation of signaling receptor activity transmembrane transport regulation of molecular function regulation of transmembrane transport positive regulation of transporter activity regulation of neurotransmitter receptor activity positive regulation of ion transmembrane transporter activity macrophage chemotaxis macrophage migration positive regulation of epithelial cell apoptotic process positive regulation of endothelial cell apoptotic process positive regulation of programmed cell death regulation of epithelial cell apoptotic process positive regulation of apoptotic process epithelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process inflammatory response cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT system process sensory perception nervous system process sensory perception of pain import into cell positive regulation of cellular component organization regulation of cellular component organization positive regulation of apoptotic cell clearance vesicle-mediated transport positive regulation of endocytosis phagocytosis apoptotic cell clearance regulation of endocytosis regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis endocytosis regulation of apoptotic cell clearance 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 immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation	extracellular region extracellular space cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth M]	IPR001811	Chemokine interleukin-8-like domain	Domain
C [auth M]	IPR000827	CC chemokine, conserved site	Conserved Site
C [auth M]	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
C [auth M]	IPR039809	Chemokine beta/gamma/delta	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth M]	Pharos: P13500	plasma cell myeloma pneumonia asthma status epilepticus Crohn disease silicosis squamous cell carcinoma Duchenne muscular dystrophy adult acute respiratory distress syndrome atherosclerosis glomerulonephritis liver disease hypertensive disorder influenza autoimmune hepatitis plasma cell myeloma pneumonia asthma status epilepticus Crohn disease silicosis squamous cell carcinoma Duchenne muscular dystrophy adult acute respiratory distress syndrome atherosclerosis glomerulonephritis liver disease hypertensive disorder influenza autoimmune hepatitis pulmonary tuberculosis calcinosis metabolic syndrome X cirrhosis of liver coronary artery disease heart valve disease retinal degeneration Liver Cirrhosis, Experimental brain ischemia spina bifida carotid artery disease inflammatory bowel disease chronic kidney disease pulmonary hypertension neural tube defect cutaneous leishmaniasis endometrial carcinoma allergic disease thyroid gland carcinoma interstitial nephritis schizophrenia HIV infectious disease cardiovascular disease tethered spinal cord syndrome middle cerebral artery infarction pleural disease thyroid adenoma congestive heart failure thyroid gland disease pulmonary fibrosis neural tube defects, susceptibility to cystic fibrosis diastematomyelia obesity disorder lung carcinoma ovarian cancer cancer malignant ependymoma pancreatic intraductal papillary-mucinous neoplasm endometrial cancer ileocolitis cerebrovascular disorder alopecia areata thrombotic disease eye disease arthritic joint disease thyroid cancer primary hyperoxaluria interstitial lung disease autoimmune disease ischemia reperfusion injury COVID-19 type 2 diabetes mellitus head and neck cancer bipolar disorder Crohn's colitis neurenteric cyst hematologic disease lung adenocarcinoma diabetic kidney disease drug-induced liver injury hyperglycemia malignant glioma adrenal cortex adenoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia susceptibility to HIV infection pilocytic astrocytoma inborn carbohydrate metabolic disorder plasma cell neoplasm pneumonitis myeloid neoplasm Gaucher disease atopic eczema psoriasis tuberculosis nasopharyngeal carcinoma juvenile dermatomyositis craniorachischisis ulcerative colitis ureteral obstruction heart disease bipolar I disorder neurodegenerative disease brain injury cutaneous lupus erythematosus non-small cell lung carcinoma breast disease skin disease lung cancer oral cavity neoplasm major depressive disorder Duchenne and Becker muscular dystrophy pancreatic intraductal papillary-mucinous carcinoma Emery-Dreifuss muscular dystrophy adrenal cortex carcinoma pancreatitis idiopathic interstitial pneumonia systemic lupus erythematosus pituitary cancer arteriosclerosis disorder iniencephaly mycobacterium tuberculosis, susceptibility to fatty liver disease interstitial cystitis myocardial ischemia glioblastoma atypical teratoid rhabdoid tumor invasive ductal breast carcinoma Becker muscular dystrophy kidney disease

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.