3DMD | pdb_00003dmd

Structures and Conformations in Solution of the Signal Recognition Particle Receptor from the archaeon Pyrococcus furiosus

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	SRP/SRP receptor N-terminal domain-like	8056580	3001834	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056581	3002018	SCOP2B (2022-06-29)
B [auth A]	SCOP2 Family	SRP54-like	8056579	4003997	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Simibi-like P-loop NTPases	8056581	3002018	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	SRP/SRP receptor N-terminal domain-like	8056580	3001834	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	SRP/SRP receptor N-terminal domain-like	8056580	3001834	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056581	3002018	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 [auth B]	DUF3228	e3dmdB3	A: a/b three-layered sandwiches	X: POZ domain	H: POZ domain	T: POZ domain	F: DUF3228	ECOD (v294.1)
B [auth A]	HSP70	e3dmdA2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (v294.1)
B [auth A]	CblD	e3dmdA4	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: CblD	ECOD (v294.1)
C	HSP70	e3dmdC2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (v294.1)
C	CblD	e3dmdC4	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: CblD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	1.20.120.140	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	SRP54, nucleotide-binding domain	CATH (4.3.0)
A [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B [auth A]	1.20.120.140	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	SRP54, nucleotide-binding domain	CATH (4.3.0)
B [auth A]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.20.120.140	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	SRP54, nucleotide-binding domain	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A], C	PF00448	SRP54-type protein, GTPase domain (SRP54)	SRP54-type protein, GTPase domain	This family includes relatives of the G-domain of the SRP54 family of proteins.	Domain
A [auth B], B [auth A], C	PF02881	SRP54-type protein, helical bundle domain (SRP54_N)	SRP54-type protein, helical bundle domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth A], C	Signal recognition particle receptor	ribonucleoprotein complex binding protein-containing complex binding binding signal recognition particle binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding ribonucleoprotein complex binding protein-containing complex binding binding signal recognition particle binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane establishment of localization protein targeting to membrane localization SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle cotranslational protein targeting to membrane cellular process establishment of protein localization to endoplasmic reticulum protein targeting to ER	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C	IPR004390	Signal-recognition particle receptor FtsY	Family
A [auth B], B [auth A], C	IPR000897	Signal recognition particle, SRP54 subunit, GTPase domain	Domain
A [auth B], B [auth A], C	IPR036225	SRP/SRP receptor, N-terminal	Homologous Superfamily
A [auth B], B [auth A], C	IPR042101	Signal recognition particle SRP54, N-terminal domain superfamily	Homologous Superfamily
A [auth B], B [auth A], C	IPR003593	AAA+ ATPase domain	Domain
A [auth B], B [auth A], C	IPR013822	Signal recognition particle SRP54, helical bundle	Domain
A [auth B], B [auth A], C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.