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	DUF903	e3fifH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF903	ECOD (1.6)
G	DUF903	e3fifG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF903	ECOD (1.6)
F	DUF903	e3fifF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF903	ECOD (1.6)
E	DUF903	e3fifE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF903	ECOD (1.6)
D	DUF903	e3fifD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF903	ECOD (1.6)
C	DUF903	e3fifC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF903	ECOD (1.6)
B	DUF903	e3fifB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF903	ECOD (1.6)
A	DUF903	e3fifA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF903	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	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	Bacterial protein of unknown function (DUF903) (DUF903)	Bacterial protein of unknown function (DUF903)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

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, SH3-like 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.