5DUD | pdb_00005dud

Crystal structure of E. coli YbgJK

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PPP2R1A-like_HEAT, VPS15-like_hel	e5dudA1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (develop294)
C	PPP2R1A-like_HEAT, VPS15-like_hel	e5dudC1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (develop294)
B	PPP2R1A-like_HEAT, VPS15-like_hel	e5dudB1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (develop294)
D	PPP2R1A-like_HEAT, VPS15-like_hel	e5dudD1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PPP2R1A-like_HEAT, VPS15-like_hel	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.100.10	Mainly Beta	Beta Barrel	Cyclophilin	Cyclophilin-like	CATH (4.3.0)
C	2.40.100.10	Mainly Beta	Beta Barrel	Cyclophilin	Cyclophilin-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF02626	Carboxyltransferase domain, subdomain A and B (CT_A_B)	Carboxyltransferase domain, subdomain A and B	-	Family
B, D	PF02682	Carboxyltransferase domain, subdomain C and D (CT_C_D)	Carboxyltransferase domain, subdomain C and D	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	YbgK	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity 5-oxoprolinase (ATP-hydrolyzing) activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B, D	YbgJ	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity 5-oxoprolinase (ATP-hydrolyzing) activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR003778	Carboxyltransferase domain, subdomain A and B	Domain
A, C	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
A, C	IPR053526	5-oxoprolinase catalytic subunit	Family
A, C	IPR052708	5-oxoprolinase subunit C	Family
B, D	IPR003833	Carboxyltransferase domain, subdomain C and D	Domain
B, D	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
B, D	IPR010016	5-oxoprolinase subunit B	Family

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.