2I9W

Crystal structure of a sec-c motif containing protein (psyc_2064) from psychrobacter arcticus at 1.75 A resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2i9wa1	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	SEC-C associated NTF2-like domain	Hypothetical protein Psyc2064	(Psychrobacter arcticus ) [TaxId: 334543 ],	SCOPe (2.08)
A	d2i9wa2	Small proteins	Sec-C motif	Sec-C motif	Sec-C motif	Hypothetical protein Psyc2064	(Psychrobacter arcticus ) [TaxId: 334543 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SEC-C associated NTF2-like domain	8022061	4001692	SCOP2 (2022-06-29)
A	SCOP2 Family	Sec-C motif	8022063	4001879	SCOP2 (2022-06-29)
A	SCOP2 Family	Sec-C motif	8022065	4001879	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NTF2-like	8034441	3000472	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sec-C motif	8034443	3000493	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sec-C motif	8034445	3000493	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)
A	PF17775	e2i9wA1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: PF17775	ECOD (1.6)
A	PF02810	e2i9wA3	A: few secondary structure elements	X: Sec-C motif (From Topology)	H: Sec-C motif (From Topology)	T: Sec-C motif	F: PF02810	ECOD (1.6)
A	PF21612	e2i9wA2	A: few secondary structure elements	X: Sec-C motif (From Topology)	H: Sec-C motif (From Topology)	T: Sec-C motif	F: PF21612	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF17775	YchJ, middle NTF2-like domain (YchJ_M-like)	YchJ, middle NTF2-like domain	This entry represents the NTF2-like domain found in the functionally uncharacterised YchJ family protein from Psychrobacter arcticus and related proteins. This domain is usually found flanked by either (Pfam:PF21612) and (Pfam:PF02810) at the N and ...	This entry represents the NTF2-like domain found in the functionally uncharacterised YchJ family protein from Psychrobacter arcticus and related proteins. This domain is usually found flanked by either (Pfam:PF21612) and (Pfam:PF02810) at the N and C terminus or flanked on both sides by (Pfam:PF02810]). The structure of YchJ shows that this domain adopts structure typical for Nuclear transport factor 2 (NTF2) that consists of a curved three-stranded beta-sheet and array of alpha-helices packed on one side of it. The function of this domain is unknown.	Domain
A	PF02810	SEC-C motif (SEC-C)	SEC-C motif	This SEC-C motif is found in the C-terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif chelates zinc with the CXC and C[HC] pairs that constitute the most conserved feature of the motif [1-2]. ...	This SEC-C motif is found in the C-terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif chelates zinc with the CXC and C[HC] pairs that constitute the most conserved feature of the motif [1-2]. In SecA, this zinc binding domain is involved in binding to SecB [2]. This domain has been also predicted to be a potential nucleic acid binding domain.	Domain
A	PF21612	YchJ family protein, N-terminal zinc binding domain (YchJ_N)	YchJ family protein, N-terminal zinc binding domain	This domain is found at the N-terminal end of the functionally uncharacterised YchJ family protein from Psychrobacter arcticus (Swiss:Q4FPZ7) and related proteins from Psychrobacter species. The structure of YchJ shows that this domain folds mainly i ...	This domain is found at the N-terminal end of the functionally uncharacterised YchJ family protein from Psychrobacter arcticus (Swiss:Q4FPZ7) and related proteins from Psychrobacter species. The structure of YchJ shows that this domain folds mainly into an alpha-helical structure. This domain contains the same type of C4 zinc finger as seen in SEC-C motif (Pfam:PF02810) located at the C terminus of YchJ which suggests a possible internal duplication in the YchJ family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Hypothetical protein	cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
A	IPR048469	YchJ-like, middle NTF2-like domain	Domain
A	IPR048463	YchJ-like, zinc-binding domain	Domain
A	IPR004027	SEC-C 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 R01GM133198.