4YXH | pdb_00004yxh

Crystal structure of Deer prion protein complexed with POM1 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
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 [auth L]	d4yxhl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d4yxhl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d4yxhh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d4yxhh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d4yxha_	Alpha and beta proteins (a+b)	Prion-like	Prion-like	Prion-like	automated matches	Mule deer (Odocoileus hemionus ) [TaxId: 9872 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Prion-like	8062984	4000908	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Prion-like	8062985	3001941	SCOP2 (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 [auth L]	Pkinase, Kdo	e4yxhL1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Pkinase, Kdo	ECOD (develop294)
B [auth H]	Pkinase, Kdo	e4yxhH2	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Pkinase, Kdo	ECOD (develop294)
B [auth H]	EF-hand_1, EF-hand_6, EF-hand_7	e4yxhH3	A: alpha bundles	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (develop294)
A	Pkinase, Kdo	e4yxhA1	A: alpha bundles	X: Cysteine proteinases-like	H: Piezo CTL2 domain	T: Piezo CTL2 domain	F: Pkinase, Kdo	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [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
C [auth L]	POM1 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV5-4801, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
B [auth H]	POM1 Fab	VH-CH1	Mus musculus (house mouse)	IGHV1S12701, IGHJ401, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L]	Light Chain	IGKV5	Kappa	major prion protein	SAbDab (2026-03-20)
B [auth H]	Heavy Chain	IGHV1	-	major prion protein	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth L]	POM1 FAB LIGHT CHAIN	-	-	-
B [auth H]	POM1 FAB HEAVY CHAIN	-	-	-
A	Major prion protein	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis	cellular anatomical structure membrane side of membrane cell periphery plasma membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020949	Prion, copper binding octapeptide repeat region	Repeat
A	IPR036924	Prion/Doppel beta-ribbon domain superfamily	Homologous Superfamily
A	IPR000817	Prion protein	Family
A	IPR025860	Major prion protein N-terminal	Domain
A	IPR022416	Prion/Doppel protein, beta-ribbon 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.