3JV2 | pdb_00003jv2

Crystal Structure of B. subtilis SecA with bound peptide

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	SCOP2B Superfamily	Pre-protein crosslinking domain of SecA	8040159	3001119	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8040163	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8040165	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8040163	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helical scaffold and wing domains of SecA	8040160	3001322	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8040165	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pre-protein crosslinking domain of SecA	8040159	3001119	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8040163	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helical scaffold and wing domains of SecA	8040160	3001322	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8040163	3002019	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	SecA_PP_bind	e3jv2A7	A: alpha arrays	X: Pre-protein crosslinking domain of SecA (From Topology)	H: Pre-protein crosslinking domain of SecA (From Topology)	T: Pre-protein crosslinking domain of SecA	F: SecA_PP_bind	ECOD (1.6)
A	SecA_SW	e3jv2A5	A: alpha complex topology	X: Helical scaffold and wing domains of SecA (From Topology)	H: Helical scaffold and wing domains of SecA (From Topology)	T: Helical scaffold and wing domains of SecA	F: SecA_SW	ECOD (1.6)
A	SecA_DEAD	e3jv2A8	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SecA_DEAD	ECOD (1.6)
A	Helicase_C_10	e3jv2A6	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_10	ECOD (1.6)
B	SecA_PP_bind	e3jv2B7	A: alpha arrays	X: Pre-protein crosslinking domain of SecA (From Topology)	H: Pre-protein crosslinking domain of SecA (From Topology)	T: Pre-protein crosslinking domain of SecA	F: SecA_PP_bind	ECOD (1.6)
B	SecA_SW	e3jv2B5	A: alpha complex topology	X: Helical scaffold and wing domains of SecA (From Topology)	H: Helical scaffold and wing domains of SecA (From Topology)	T: Helical scaffold and wing domains of SecA	F: SecA_SW	ECOD (1.6)
B	SecA_DEAD	e3jv2B8	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SecA_DEAD	ECOD (1.6)
B	Helicase_C_10	e3jv2B6	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_10	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	1.10.3060.10	Mainly Alpha	Orthogonal Bundle	Helical scaffold and wing domains of SecA	Helical scaffold and wing domains of SecA	CATH (utative)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
B	3.90.1440.10	Alpha Beta	Alpha-Beta Complex	Pre-protein croslinking domain of SecA	SecA, preprotein cross-linking domain	CATH (utative)
B	1.10.3060.10	Mainly Alpha	Orthogonal Bundle	Helical scaffold and wing domains of SecA	Helical scaffold and wing domains of SecA	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01043	SecA preprotein cross-linking domain (SecA_PP_bind)	SecA preprotein cross-linking domain	The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domai ...	The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain [1].	Domain
A, B	PF07516	SecA Wing and Scaffold domain (SecA_SW)	SecA Wing and Scaffold domain	-	Family
A, B	PF21090	SecA P-loop domain (P-loop_SecA)	SecA P-loop domain	SecA is the preprotein translocase ATPase subunit and a superfamily 2 (SF2) RNA helicase [4]. This entry corresponds to the second P-loop domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Protein translocase subunit SecA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity protein transmembrane transporter activity protein-transporting ATPase activity protein-exporting ATPase activity ATP-dependent activity macromolecule transmembrane transporter activity active transmembrane transporter activity transporter activity transmembrane transporter activity cation binding metal ion binding	protein import localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization protein targeting cellular localization intracellular protein transmembrane transport intracellular transport transmembrane transport protein import localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization protein targeting cellular localization intracellular protein transmembrane transport intracellular transport transmembrane transport protein transmembrane transport establishment of localization in cell cellular process intracellular protein transport protein transport by the Sec complex	cell periphery cellular anatomical structure plasma membrane membrane membrane microdomain membrane raft protein-containing complex cell envelope Sec protein transport complex intracellular protein-containing complex intracellular anatomical structure cytoplasm
C, D	peptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011130	SecA, preprotein cross-linking domain	Domain
A, B	IPR011116	SecA Wing/Scaffold	Domain
A, B	IPR036266	SecA, Wing/Scaffold superfamily	Homologous Superfamily
A, B	IPR001650	Helicase, C-terminal domain-like	Domain
A, B	IPR000185	Protein translocase subunit SecA	Family
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR004027	SEC-C motif	Conserved Site
A, B	IPR014018	SecA motor DEAD	Domain
A, B	IPR020937	SecA conserved site	Conserved Site
A, B	IPR011115	SecA DEAD-like, N-terminal	Domain
A, B	IPR044722	SecA, C-terminal helicase domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR036670	SecA, preprotein cross-linking domain superfamily	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.