4RK1 | pdb_00004rk1

Crystal structure of LacI family transcriptional regulator from Enterococcus faecium, Target EFI-512930, with bound ribose

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
F	d4rk1f_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Enterococcus faecium DO ) [TaxId: 333849 ],	SCOPe (2.08)
E	d4rk1e_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Enterococcus faecium DO ) [TaxId: 333849 ],	SCOPe (2.08)
D	d4rk1d_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Enterococcus faecium DO ) [TaxId: 333849 ],	SCOPe (2.08)
C	d4rk1c_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Enterococcus faecium DO ) [TaxId: 333849 ],	SCOPe (2.08)
B	d4rk1b_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Enterococcus faecium DO ) [TaxId: 333849 ],	SCOPe (2.08)
A	d4rk1a_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Enterococcus faecium DO ) [TaxId: 333849 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Peptidase_S41	e4rk1F1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Peptidase_S41	ECOD (v294.1)
F	Glyco_hydro_106	e4rk1F2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (v294.1)
E	Peptidase_S41	e4rk1E1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Peptidase_S41	ECOD (v294.1)
E	Glyco_hydro_106	e4rk1E2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (v294.1)
D	Peptidase_S41	e4rk1D1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Peptidase_S41	ECOD (v294.1)
D	Glyco_hydro_106	e4rk1D2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (v294.1)
C	Peptidase_S41	e4rk1C1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Peptidase_S41	ECOD (v294.1)
C	Glyco_hydro_106	e4rk1C2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (v294.1)
B	Peptidase_S41	e4rk1B1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Peptidase_S41	ECOD (v294.1)
B	Glyco_hydro_106	e4rk1B2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (v294.1)
A	Peptidase_S41	e4rk1A1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Peptidase_S41	ECOD (v294.1)
A	Glyco_hydro_106	e4rk1A2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
E	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
D	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)

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	Ribose transcriptional regulator	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR001387	Cro/C1-type, helix-turn-helix domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000843	LacI-type HTH domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001761	Periplasmic binding protein/LacI sugar binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR010982	Lambda repressor-like, DNA-binding 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.