1VKM

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution

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)
A	d1vkma1	Alpha and beta proteins (a/b)	Indigoidine synthase A-like	Indigoidine synthase A-like	Indigoidine synthase A-like	Hypothetical protein TM1464	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d1vkma2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
C	d1vkmc1	Alpha and beta proteins (a/b)	Indigoidine synthase A-like	Indigoidine synthase A-like	Indigoidine synthase A-like	Hypothetical protein TM1464	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
C	d1vkmc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
D	d1vkmd1	Alpha and beta proteins (a/b)	Indigoidine synthase A-like	Indigoidine synthase A-like	Indigoidine synthase A-like	Hypothetical protein TM1464	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
D	d1vkmd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d1vkmb1	Alpha and beta proteins (a/b)	Indigoidine synthase A-like	Indigoidine synthase A-like	Indigoidine synthase A-like	Hypothetical protein TM1464	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d1vkmb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E	d1vkme1	Alpha and beta proteins (a/b)	Indigoidine synthase A-like	Indigoidine synthase A-like	Indigoidine synthase A-like	Hypothetical protein TM1464	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E	d1vkme2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
F	d1vkmf1	Alpha and beta proteins (a/b)	Indigoidine synthase A-like	Indigoidine synthase A-like	Indigoidine synthase A-like	Hypothetical protein TM1464	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
F	d1vkmf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Indigoidine synthase A-like	8029013	4002186	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Indigoidine synthase A-like	8041392	3000924	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Indigoidine synthase A-like	8041392	3000924	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Indigoidine synthase A-like	8041392	3000924	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Indigoidine synthase A-like	8041392	3000924	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Indigoidine synthase A-like	8041392	3000924	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Indigoidine synthase A-like	8041392	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)
A	Indigoidine_A	e1vkmA1	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)
C	Indigoidine_A	e1vkmC1	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)
D	Indigoidine_A	e1vkmD1	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	e1vkmB1	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)
E	Indigoidine_A	e1vkmE1	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)
F	Indigoidine_A	e1vkmF1	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)
A	3.40.1790.10	Alpha Beta	3-Layer(aba) Sandwich	Indigoidine synthase fold	Indigoidine synthase domain	CATH (4.3.0)
C	3.40.1790.10	Alpha Beta	3-Layer(aba) Sandwich	Indigoidine synthase fold	Indigoidine synthase domain	CATH (4.3.0)
D	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)
E	3.40.1790.10	Alpha Beta	3-Layer(aba) Sandwich	Indigoidine synthase fold	Indigoidine synthase domain	CATH (4.3.0)
F	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, D, E A, B, C, D, E, F	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, D, E A, B, C, D, E, F	conserved hypothetical protein TM1464	hydro-lyase activity lyase activity pseudouridylate synthase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds hydrolase activity cation binding ion binding binding metal ion binding small molecule 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 primary metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR007342	Pseudouridine-5'-phosphate glycosidase	Family
A, B, C, D, E A, B, C, D, E, F	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.