6DDR | pdb_00006ddr

Crystal Structure Analysis of the Epitope of an Anti-MICA Antibody

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d6ddrc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6ddrb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d6ddrb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d6ddra2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d6ddra1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8100402	3000071	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)
C	C1-set_2	e6ddrC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
B	V-set_8	e6ddrB2	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	e6ddrB1	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)
A	C1-set_4	e6ddrA2	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	e6ddrA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	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	Beta-2 Microglobulin	B2M	Homo sapiens (human)	MICA10, MICA19, MICA22, MICA27, MICA33, MICA35, MICA37, MICA42, MICA48, MICA55, MICA66, MICA68, MICA70, MICA75, MICA*76	C-LIKE-DOMAIN C-LIKE	RPI	B2M	IMGT (202542-0)
B	Fab13A9, anti-MICA	VH-CH1	Mus musculus (house mouse)	IGHV1-5402, IGHV1-5403, IGHJ201, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202542-0)
A	Fab13A9, anti-MICA	L-KAPPA	Mus musculus (house mouse)	IGKV12-4102, IGKV12-4101, IGKJ201, IGKC03	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202542-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	mhc class i polypeptide-related sequence a	SAbDab (2025-10-31)
A	Light Chain	IGKV12	Kappa	mhc class i polypeptide-related sequence a	SAbDab (2025-10-31)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	MHC class I polypeptide-related sequence A	natural killer cell lectin-like receptor binding protein binding binding signaling receptor binding cation binding ion binding metal ion binding small molecule binding	multicellular organismal process gamma-delta T cell activation T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing regulation of biological process multicellular organismal process gamma-delta T cell activation T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing regulation of biological process response to stimulus regulation of response to stimulus immune response biological regulation regulation of immune response regulation of immune system process regulation of defense response negative regulation of response to stimulus defense response negative regulation of biological process regulation of response to stress response to stress negative regulation of defense response response to heat response to abiotic stimulus response to temperature stimulus	cell periphery cellular anatomical structure plasma membrane membrane
B	Anti-MICA Fab fragment heavy chain clone 13A9	-	-	-
A	Anti-MICA Fab fragment light chain clone 13A9	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C	IPR050208	Antigen-presenting and immune regulatory MHC class I-related	Family
C	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
C	IPR003597	Immunoglobulin C1-set	Domain
C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C	IPR011161	MHC class I-like antigen recognition-like	Domain
C	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
C	IPR007110	Immunoglobulin-like domain	Domain

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.