4DKF | pdb_00004dkf

Crystal Structure of Human Interleukin-34 Bound to FAb2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody 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)
D [auth L]	d4dkfl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d4dkfl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth M]	d4dkfm2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth M]	d4dkfm1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4dkfA1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: V-set	F:	ECOD (20:10:01)
B		e4dkfB1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: V-set	F:	ECOD (20:10:01)
C [auth H]		e4dkfH1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: Sushi	F:	ECOD (20:10:01)
E [auth I]		e4dkfI3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: V-set	F:	ECOD (20:10:01)
D [auth L]		e4dkfL1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: Sushi	F:	ECOD (20:10:01)
F [auth M]		e4dkfM1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: 14-3-3	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1250.80	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
B	1.20.1250.80	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth M]	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
C [auth H], E [auth I]	FAb2	VH-CH1	Homo sapiens (human)	IGHV3-2304, IGHJ601, IGHJ602, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)
D [auth L], F [auth M]	FAb2	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], E [auth I]	Heavy Chain	IGHV3	-	interleukin-34	SAbDab (2026-03-13)
D [auth L], F [auth M]	Light Chain	IGKV1	Kappa	interleukin-34	SAbDab (2026-03-13)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Interleukin-34	protein binding binding signaling receptor binding cytokine receptor binding macrophage colony-stimulating factor receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity growth factor activity identical protein binding	cellular response to stimulus positive regulation of locomotion regulation of cell motility regulation of cellular process response to stimulus macrophage migration positive regulation of chemotaxis positive regulation of cell migration taxis cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process chemotaxis cellular response to stimulus positive regulation of locomotion regulation of cell motility regulation of cellular process response to stimulus macrophage migration positive regulation of chemotaxis positive regulation of cell migration taxis 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 regulation of leukocyte migration positive regulation of macrophage migration response to external stimulus positive regulation of leukocyte chemotaxis granulocyte migration leukocyte migration regulation of response to stimulus response to chemical regulation of locomotion regulation of response to external stimulus macrophage chemotaxis positive regulation of biological process positive regulation of response to stimulus regulation of granulocyte chemotaxis regulation of macrophage migration positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration myeloid leukocyte migration positive regulation of mononuclear cell migration cell motility locomotion positive regulation of cellular process cell chemotaxis regulation of macrophage chemotaxis biological regulation positive regulation of leukocyte migration regulation of chemotaxis cellular response to chemical stimulus immune system process granulocyte chemotaxis mononuclear cell migration positive regulation of macrophage chemotaxis cellular process leukocyte chemotaxis cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation cell surface receptor signaling pathway signaling response to cytokine cytokine-mediated signaling pathway cell communication response to peptide cellular response to cytokine stimulus signal transduction interleukin-34-mediated signaling pathway positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication positive regulation of signaling regulation of leukocyte proliferation leukocyte proliferation macrophage proliferation positive regulation of leukocyte proliferation positive regulation of macrophage proliferation regulation of macrophage proliferation multicellular organismal process myeloid leukocyte differentiation regulation of leukocyte differentiation positive regulation of monocyte differentiation cellular developmental process regulation of developmental process cell development regulation of cell differentiation mononuclear cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation positive regulation of hemopoiesis cell differentiation anatomical structure development regulation of multicellular organismal process monocyte differentiation developmental process regulation of multicellular organismal development regulation of monocyte differentiation hemopoiesis regulation of myeloid cell differentiation positive regulation of cell development regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation myeloid cell differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of multicellular organismal process positive regulation of leukocyte differentiation leukocyte differentiation regulation of biosynthetic 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 microglial cell proliferation nervous system development neurogenesis gliogenesis glial cell proliferation system development regulation of macrophage differentiation macrophage differentiation positive regulation of macrophage differentiation positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation defense response response to stress inflammatory response biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont response to biotic stimulus defense response to other organism innate immune response response to external biotic stimulus positive regulation of nervous system development regulation of neurogenesis regulation of gliogenesis positive regulation of gliogenesis regulation of nervous system development positive regulation of neurogenesis positive regulation of oligodendrocyte differentiation regulation of glial cell differentiation positive regulation of glial cell differentiation central nervous system development oligodendrocyte differentiation glial cell differentiation regulation of oligodendrocyte differentiation	cellular anatomical structure extracellular region extracellular space
C [auth H], E [auth I]	FAb2 Heavy Chain	-	-	-
D [auth L], F [auth M]	FAb2 Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR038328	Interleukin-34 superfamily	Homologous Superfamily
A, B	IPR020415	Interleukin-34	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q6ZMJ4	polycystic ovary syndrome atypical teratoid rhabdoid tumor large cell medulloblastoma ovarian cancer psoriasis glioblastoma malignant glioma peripheral neuropathy Sclerocystic Ovaries juvenile dermatomyositis medulloblastoma Sjogren syndrome

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.