3FIF | pdb_00003fif

Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.

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)
H	d3fifh1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	YgdI/YgdR-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
H	d3fifh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G	d3fifg1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	YgdI/YgdR-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G	d3fifg2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d3fiff1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	YgdI/YgdR-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d3fiff2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d3fife1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	YgdI/YgdR-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d3fife2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3fifd1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	YgdI/YgdR-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3fifd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3fifc1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	YgdI/YgdR-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3fifc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3fifb1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	YgdI/YgdR-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3fifb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3fifa1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	YgdI/YgdR-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3fifa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Sm-like ribonucleoproteins	8034699	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8034699	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8034699	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8034699	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8034699	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8034699	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8034699	3000419	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8034699	3000419	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)
H	IL7	e3fifH1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.2)
G	IL7	e3fifG1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.2)
F	IL7	e3fifF1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.2)
E	IL7	e3fifE1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.2)
D	IL7	e3fifD1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.2)
C	IL7	e3fifC1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.2)
B	IL7	e3fifB1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.2)
A	IL7	e3fifA1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
H	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
G	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
F	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
E	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
D	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
C	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
B	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF06004	Domain of unknown function (DUF903) (DUF903)	Domain of unknown function (DUF903)	This family consists of several small bacterial proteins including the uncharacterized lipoproteins YgdI and YgdR. The function of these proteins is unknown.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Uncharacterized lipoprotein ygdR	-	-	cell periphery cellular anatomical structure plasma membrane membrane
I [auth Y]	Uncharacterized ligand	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010920	LSM domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010305	Lipoprotein YgdI/YgdR-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR047807	Lipoprotein YgdI/YgdR-like, Sm-like domain	Domain

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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.