4GIM | pdb_00004gim

Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-phosphate

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Indigoidine synthase A-like	8089538	3000924	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Indigoidine synthase A-like	8089538	3000924	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Indigoidine synthase A-like	8089538	3000924	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)
C	Indigoidine_A	e4gimC1	A: a/b three-layered sandwiches	X: Indigoidine synthase A-like (Pfam 04227) (From Topology)	H: Indigoidine synthase A-like (Pfam 04227) (From Topology)	T: Indigoidine synthase A-like (Pfam 04227)	F: Indigoidine_A	ECOD (1.6)
B	Indigoidine_A	e4gimB1	A: a/b three-layered sandwiches	X: Indigoidine synthase A-like (Pfam 04227) (From Topology)	H: Indigoidine synthase A-like (Pfam 04227) (From Topology)	T: Indigoidine synthase A-like (Pfam 04227)	F: Indigoidine_A	ECOD (1.6)
A	Indigoidine_A	e4gimA1	A: a/b three-layered sandwiches	X: Indigoidine synthase A-like (Pfam 04227) (From Topology)	H: Indigoidine synthase A-like (Pfam 04227) (From Topology)	T: Indigoidine synthase A-like (Pfam 04227)	F: Indigoidine_A	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.1790.10	Alpha Beta	3-Layer(aba) Sandwich	Indigoidine synthase fold	Indigoidine synthase domain	CATH (4.3.0)
B	3.40.1790.10	Alpha Beta	3-Layer(aba) Sandwich	Indigoidine synthase fold	Indigoidine synthase domain	CATH (4.3.0)
A	3.40.1790.10	Alpha Beta	3-Layer(aba) Sandwich	Indigoidine synthase fold	Indigoidine synthase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF04227	Indigoidine synthase A like protein (Indigoidine_A)	Indigoidine synthase A like protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Pseudouridine-5'-phosphate glycosidase	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity pseudouridylate synthase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds hydrolase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity pseudouridylate synthase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds hydrolase activity identical protein binding protein binding	nucleobase-containing compound metabolic process catabolic process nucleobase catabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR007342	Pseudouridine-5'-phosphate glycosidase	Family
A, B, C	IPR022830	Indigoidine synthase A-like	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.