1DEE | pdb_00001dee

Structure of S. aureus protein A bound to a human IgM Fab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
H	d1deeh_	All alpha proteins	immunoglobulin/albumin-binding domain-like	Bacterial immunoglobulin/albumin-binding domains	Immunoglobulin-binding protein A modules	Immunoglobulin-binding protein A modules	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
G	d1deeg_	All alpha proteins	immunoglobulin/albumin-binding domain-like	Bacterial immunoglobulin/albumin-binding domains	Immunoglobulin-binding protein A modules	Immunoglobulin-binding protein A modules	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
F	d1deef1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1deef2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain mu constant domain 1, CH1-mu	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1deed1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1deed2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain mu constant domain 1, CH1-mu	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1deeb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1deeb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain mu constant domain 1, CH1-mu	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1deee1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1deee2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1deec1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1deec2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1deea1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1deea2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	(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)
H	Alpha-2-MRAP_N	e1deeH1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: Alpha-2-MRAP_N	ECOD (v294.1)
G	Alpha-2-MRAP_N	e1deeG1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: Alpha-2-MRAP_N	ECOD (v294.1)
F	Copper-bind	e1deeF1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
D	Copper-bind	e1deeD1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
B	Copper-bind	e1deeB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
E	Copper-bind	e1deeE1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
C	Copper-bind	e1deeC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
A	Copper-bind	e1deeA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.20.5.420	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Immunoglobulin FC, subunit C	CATH (4.3.0)
G	1.20.5.420	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Immunoglobulin FC, subunit C	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	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)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	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
B, D, F	IgmRf2A2	VH-CH1	Homo sapiens (human)	IGHV3-3018, IGHJ401, IGHJ402, IGHJ403, IGHM*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-MU_KAPPA	IMGT (202611-0)
A, C, E	IgmRf2A2	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-MU_KAPPA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D, F	Heavy Chain	IGHV3	-	immunoglobulin g binding protein a	SAbDab (2026-03-27)
A, C, E	Light Chain	IGKV1	Kappa	immunoglobulin g binding protein a	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G, H	PF02216	B domain (B)	B domain	This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H	IMMUNOGLOBULIN G BINDING PROTEIN A	protein-containing complex binding binding immunoglobulin binding IgG binding	symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host signal transduction pathway via antagonism of host cell surface receptor symbiont-mediated perturbation of host process symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction	cellular anatomical structure extracellular region
B, D, F	IGM RF 2A2	-	-	-
A, C, E	IGM RF 2A2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
G, H	IPR005877	YSIRK Gram-positive signal peptide	Domain
G, H	IPR036779	LysM domain superfamily	Homologous Superfamily
G, H	IPR005038	Octapeptide repeat	Repeat
G, H	IPR003132	Protein A, Ig-binding domain	Domain
G, H	IPR018392	LysM domain	Domain
G, H	IPR019931	LPXTG cell wall anchor motif	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.