5IKC | pdb_00005ikc

X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5ikca2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d5ikca1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d5ikca3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth L]	d5ikcl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth L]	d5ikcl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth L]	d5ikcl3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d5ikcb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d5ikcb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth H]	d5ikch1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth H]	d5ikch2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth M]	d5ikcm1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Doublecortin (DC)	Doublecortin (DC)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth M]	d5ikcm2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth N]	d5ikcn1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Doublecortin (DC)	Doublecortin (DC)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth N]	d5ikcn2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
E [auth M]	SCOP2B Superfamily	Doublecortin (DC)	8032858	3000670	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	Doublecortin (DC)	8032858	3000670	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	C1-set_4	e5ikcA2	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	V-set	e5ikcA1	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 L]	C1-set_4	e5ikcL1	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)
D [auth L]	V-set	e5ikcL2	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	V-set_8	e5ikcB1	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	C1-set_1	e5ikcB2	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 H]	V-set_8	e5ikcH2	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)
C [auth H]	C1-set_1	e5ikcH1	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)
E [auth M]	DCX	e5ikcM1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DCX	ECOD (1.6)
F [auth N]	DCX	e5ikcN1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DCX	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth M]	3.10.20.230	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Doublecortin domain	CATH (4.3.0)
F [auth N]	3.10.20.230	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Doublecortin domain	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, D [auth L]	mAb 6H10	L-KAPPA	Mus musculus (house mouse)	IGKV6-1401, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2B_KAPPA	IMGT (202510-0)
B, C [auth H]	mAb 6H10	VH-CH1	Mus musculus (house mouse)	IGHV14-302, IGHJ201, 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
A, D [auth L]	Light Chain	IGKV6	Kappa	neuronal migration protein doublecortin	SAbDab (2025-03-21)
B, C [auth H]	Heavy Chain	IGHV14	-	neuronal migration protein doublecortin	SAbDab (2025-03-21)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth L]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A, D [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
B, C [auth H]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B, C [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
E [auth M], F [auth N]	PF03607	Doublecortin (DCX)	Doublecortin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth L]	MAb 6H10 light chain	-	-	-
B, C [auth H]	Ighg protein	-	-	-
E [auth M], F [auth N]	Neuronal migration protein doublecortin	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding kinase binding enzyme binding protein kinase binding	developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development sensory organ development eye development animal organ development retina development in camera-type eye visual system development camera-type eye development sensory system development developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development sensory organ development eye development animal organ development retina development in camera-type eye visual system development camera-type eye development sensory system development neuron migration cellular developmental process generation of neurons neurogenesis cell differentiation cellular process cell migration cell motility cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction intracellular signal transduction cell communication organelle assembly plasma membrane bounded cell projection organization cell projection organization microtubule cytoskeleton organization plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis microtubule bundle formation organelle organization cellular component assembly cilium assembly microtubule-based process cellular component organization or biogenesis axoneme assembly cytoskeleton organization cilium organization cell projection assembly	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle cytoplasm cytosol protein-containing complex microtubule associated complex microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle cytoplasm cytosol protein-containing complex microtubule associated complex microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex cell projection neuron projection plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth L]	IPR003597	Immunoglobulin C1-set	Domain
A, D [auth L]	IPR050150	Immunoglobulin Variable Light Chain	Family
A, D [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, D [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, D [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
A, D [auth L]	IPR003599	Immunoglobulin domain subtype	Domain
A, D [auth L]	IPR007110	Immunoglobulin-like domain	Domain
A, D [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B, C [auth H]	IPR003597	Immunoglobulin C1-set	Domain
B, C [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, C [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, C [auth H]	IPR013106	Immunoglobulin V-set domain	Domain
B, C [auth H]	IPR003599	Immunoglobulin domain subtype	Domain
B, C [auth H]	IPR007110	Immunoglobulin-like domain	Domain
B, C [auth H]	IPR050380	Immune Recognition and Response Modulators	Family
B, C [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
E [auth M], F [auth N]	IPR003533	Doublecortin domain	Domain
E [auth M], F [auth N]	IPR017302	Neuronal migration protein doublecortin, chordates	Family
E [auth M], F [auth N]	IPR036572	Doublecortin domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth M], F [auth N]	Pharos: O43602	subcortical band heterotopia lissencephaly spectrum disorders lissencephaly type 1 due to doublecortin gene mutation Miller-Dieker lissencephaly syndrome oligodendroglioma pituitary cancer arthrogryposis cerebrovascular disorder Classical Lissencephaly intellectual disability lung carcinoma medulloblastoma ovarian cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor subcortical band heterotopia lissencephaly spectrum disorders lissencephaly type 1 due to doublecortin gene mutation Miller-Dieker lissencephaly syndrome oligodendroglioma pituitary cancer arthrogryposis cerebrovascular disorder Classical Lissencephaly intellectual disability lung carcinoma medulloblastoma ovarian cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor chromosome 17p13.1 deletion syndrome epilepsy invasive ductal breast carcinoma Pick disease progressive supranuclear palsy breast cancer malignant ependymoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, C [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.