5D70

Crystal structure of MOR03929, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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	d5d70a1	All alpha proteins	4-helical cytokines	4-helical cytokines	Short-chain cytokines	Granulocyte-macrophage colony-stimulating factor (GM-CSF)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5d70a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d5d70l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	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)
A	SCOP2B Superfamily	4-helical cytokines	8037087	3001717	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	GM_CSF	e5d70A1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: GM_CSF	ECOD (1.6)
B [auth H]	V-set_8	e5d70H2	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	e5d70H1	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 L]	C1-set	e5d70L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
C [auth L]	V-set_3	e5d70L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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
B [auth H]	MOR03929 Fab, anti-human GM-CSF, neutralizing	VH-CH1	Homo sapiens (human)	IGHV3-4803, IGHV3-2304, IGHJ401, IGHJ601, IGHJ402, IGHJ403, IGHJ602, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202415-0)
C [auth L]	MOR03929 Fab, anti-human GM-CSF, neutralizing	L-LAMBDA	Homo sapiens (human)	IGLV3-101, IGLJ201, IGLJ301, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV3	-	granulocyte-macrophage colony-stimulating factor	SAbDab (2024-04-19)
C [auth L]	Light Chain	IGLV3	Lambda	granulocyte-macrophage colony-stimulating factor	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01109	Granulocyte-macrophage colony-stimulating factor (GM_CSF)	Granulocyte-macrophage colony-stimulating factor	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Granulocyte-macrophage colony-stimulating factor	protein binding binding signaling receptor binding cytokine receptor binding growth factor receptor binding granulocyte macrophage colony-stimulating factor receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cytokine activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process cellular response to stimulus negative regulation of extrinsic apoptotic signaling pathway in absence of ligand response to stimulus signal transduction in absence of ligand negative regulation of signaling signaling 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 cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway extrinsic apoptotic signaling pathway in absence of ligand signal transduction regulation of signaling cell surface receptor signaling pathway 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 developmental process multicellular organismal process myeloid leukocyte differentiation cellular developmental process myeloid dendritic cell activation hemopoiesis cell activation cell development mononuclear cell differentiation myeloid leukocyte activation leukocyte activation myeloid cell differentiation immune system process cell differentiation anatomical structure development myeloid dendritic cell differentiation dendritic cell differentiation leukocyte differentiation granulocyte differentiation neutrophil differentiation immune response positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of gene expression positive regulation of cellular biosynthetic process rhythmic process circadian sleep/wake cycle, sleep circadian sleep/wake cycle rhythmic behavior regulation of circadian sleep/wake cycle circadian rhythm regulation of circadian rhythm regulation of behavior behavior circadian behavior regulation of multicellular organismal process sleep regulation of circadian sleep/wake cycle, sleep circadian sleep/wake cycle process cell population proliferation localization epithelial fluid transport transport transepithelial transport fluid transport establishment of localization response to organic substance biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus 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 cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid cellular response to organic substance response to external biotic stimulus response to molecule of bacterial origin placenta development chordate embryonic development animal organ development embryo development in utero embryonic development multicellular organism development embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development regulation of developmental process macrophage derived foam cell differentiation regulation of cell differentiation positive regulation of developmental process foam cell differentiation positive regulation of cell differentiation regulation of macrophage derived foam cell differentiation positive regulation of macrophage derived foam cell differentiation response to silicon dioxide response to inorganic substance nitrogen compound transport secretion histamine transport organic substance transport histamine secretion positive regulation of cell population proliferation regulation of cell population proliferation response to granulocyte macrophage colony-stimulating factor response to cytokine cellular response to granulocyte macrophage colony-stimulating factor stimulus cellular response to cytokine stimulus macrophage differentiation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of phosphorylation positive regulation of phosphate metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation tyrosine phosphorylation of STAT protein protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process macromolecule modification regulation of phosphorus metabolic process cell surface receptor signaling pathway via STAT regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process peptidyl-tyrosine modification positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process protein metabolic process organonitrogen compound metabolic process regulation of tyrosine phosphorylation of STAT protein regulation of peptidyl-tyrosine phosphorylation positive regulation of tyrosine phosphorylation of STAT protein regulation of phosphorylation peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT cytokine production regulation of cytokine production positive regulation of interleukin-23 production interleukin-23 production positive regulation of multicellular organismal process regulation of interleukin-23 production positive regulation of cytokine production monocyte differentiation positive regulation of organelle organization positive regulation of cellular component organization regulation of cellular component organization non-membrane-bounded organelle assembly positive regulation of podosome assembly cellular component biogenesis cellular component organization positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly regulation of podosome assembly protein-containing complex assembly cellular component organization or biogenesis organelle assembly podosome assembly positive regulation of cellular component biogenesis protein-containing complex organization regulation of cellular component biogenesis regulation of organelle organization organelle organization regulation of organelle assembly positive regulation of organelle assembly cytokine-mediated signaling pathway granulocyte-macrophage colony-stimulating factor signaling pathway regulation of leukocyte proliferation leukocyte proliferation positive regulation of leukocyte proliferation response to stress response to fluid shear stress	cell periphery plasma membrane membrane cellular anatomical entity membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex granulocyte macrophage colony-stimulating factor receptor complex cell periphery plasma membrane membrane cellular anatomical entity membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex granulocyte macrophage colony-stimulating factor receptor complex receptor complex extracellular region extracellular space
B [auth H]	Immunglobulin G1 Fab fragment, heavy chain	-	-	-
C [auth L]	Immunglobulin G1 Fab fragment, light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000773	Granulocyte-macrophage colony-stimulating factor	Family
A	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P04141	rheumatoid arthritis neutropenia psoriasis thrombocytopenia juvenile myelomonocytic leukemia agranulocytosis plasma cell myeloma melanoma aplastic anemia acute myeloid leukemia pneumonia neural tube defect colorectal cancer spindle cell sarcoma congestive heart failure rheumatoid arthritis neutropenia psoriasis thrombocytopenia juvenile myelomonocytic leukemia agranulocytosis plasma cell myeloma melanoma aplastic anemia acute myeloid leukemia pneumonia neural tube defect colorectal cancer spindle cell sarcoma congestive heart failure liver cancer thyroid gland carcinoma Venous Thrombosis anemia pulmonary fibrosis breast carcinoma sarcoma carcinoma non-alcoholic fatty liver disease thyroid adenoma visceral leishmaniasis bone marrow failure syndrome sarcomatoid carcinoma dissociative amnesia myeloid neoplasm breast cancer cancer schizophrenia hypereosinophilic syndrome idiopathic interstitial pneumonia cutaneous melanoma pancytopenia-developmental delay syndrome diastematomyelia amnestic disorder pneumonitis asthma gastrointestinal mucositis bone marrow disease skin disease colorectal carcinoma craniorachischisis influenza cystic fibrosis liver neoplasm peripheral nervous system disease lymphatic system disease allergic disease plasma cell neoplasm autoimmune disease reticulum cell sarcoma heart failure breast disease neurenteric cyst non-Hodgkin lymphoma inflammatory bowel disease Crohn disease tethered spinal cord syndrome iniencephaly thyroid cancer leukopenia peripheral neuropathy undifferentiated carcinoma epithelioid sarcoma pulmonary alveolar proteinosis eyelid disease lymphosarcoma arthritic joint disease pustulosis palmaris et plantaris autosomal dominant aplasia and myelodysplasia

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.