3E3M | pdb_00003e3m

Crystal structure of a LacI family transcriptional regulator from Silicibacter pomeroyi

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d3e3ma1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
A	d3e3ma2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
B	d3e3mb1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
B	d3e3mb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
C	d3e3mc1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
C	d3e3mc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
D	d3e3md1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
D	d3e3md2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ALO	e3e3mA2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ALO	ECOD (develop294)
A	Peripla_BP_2	e3e3mA3	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Peripla_BP_2	ECOD (develop294)
B	ALO	e3e3mB2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ALO	ECOD (develop294)
B	Peripla_BP_2	e3e3mB1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Peripla_BP_2	ECOD (develop294)
C	ALO	e3e3mC2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ALO	ECOD (develop294)
C	Peripla_BP_2	e3e3mC1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Peripla_BP_2	ECOD (develop294)
D	ALO	e3e3mD2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ALO	ECOD (develop294)
D	Peripla_BP_2	e3e3mD3	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Peripla_BP_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
C	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13377	Periplasmic binding protein-like domain (Peripla_BP_3)	Periplasmic binding protein-like domain	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule liga ...	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognises Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Transcriptional regulator, LacI family	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	IPR046335	Transcriptional regulator LacI/GalR-like, sensor domain	Domain
A, B, C, D	IPR000843	LacI-type HTH domain	Domain
A, B, C, D	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B, C, D	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.