1VKM | pdb_00001vkm

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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	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)
D	SCOP2B Superfamily	Indigoidine synthase A-like	8041392	3000924	SCOP2B (2022-06-29)
C	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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Pribosyltran	e1vkmF1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
E	Pribosyltran	e1vkmE1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
D	Pribosyltran	e1vkmD1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
C	Pribosyltran	e1vkmC1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
B	Pribosyltran	e1vkmB1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (develop294)
A	Indigoidine_A	e1vkmA1	A: alpha bundles	X: Indigoidine synthase A-like (Pfam 04227)	H: Indigoidine synthase A-like (Pfam 04227)	T: Indigoidine synthase A-like (Pfam 04227)	F: Indigoidine_A	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
D	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)
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, 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 cellular process primary metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.