5VKK | pdb_00005vkk

Crystal structure of Fab fragment of anti-CD22 Epratuzumab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody 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)
D [auth B]	d5vkkb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d5vkkb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d5vkkl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d5vkkl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d5vkka_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth H]	d5vkkh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ], 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)
D [auth B]	PK_Tyr_Ser-Thr	e5vkkB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
B [auth L]	PK_Tyr_Ser-Thr	e5vkkL1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
C [auth A]	PK_Tyr_Ser-Thr	e5vkkA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
A [auth H]	PK_Tyr_Ser-Thr	e5vkkH1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PK_Tyr_Ser-Thr	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth H]	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 L], D [auth B]	Fab Epratuzumab, anti-CD22	L-KAPPA	Homo sapiens (human)	IGKV4-101, IGKJ401, IGKJ202, IGKJ402, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202611-0)
A [auth H], C [auth A]	Fab Epratuzumab, anti-CD22	VH-CH1	Homo sapiens (human)	IGHV1-301, IGHV1-4601, IGHV1-4603, IGHV1-6901, IGHV1-6911, IGHV1-6912, IGHV1-6913, IGHV1-69D01, IGHV1-6915, IGHJ601, IGHG103, IGHG108, IGHG1*06	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L], D [auth B]	Light Chain	IGKV8	Kappa	-	SAbDab (2026-03-27)
A [auth H], C [auth A]	Heavy Chain	IGHV1	-	-	SAbDab (2026-03-27)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B [auth L], D [auth B]	Epratuzumab	SIGLEC2/CD22	Therapeutic SAbDab (2026-03-27)
A [auth H], C [auth A]	Epratuzumab	SIGLEC2/CD22	Therapeutic SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth L], D [auth B]	Epratuzumab Fab Light Chain	cation binding ion binding binding metal ion binding small molecule binding	response to stimulus immune response immune system process adaptive immune response	cellular anatomical structure extracellular region cell periphery plasma membrane membrane protein-containing complex immunoglobulin complex
A [auth H], C [auth A]	Epratuzumab Fab Heavy Chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

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

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.