1VBK | pdb_00001vbk

Crystal structure of PH1313 from Pyrococcus horikoshii Ot3

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d1vbka1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	ThiI-like	Hypothetical protein PH1313, C-terminal domain	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
A	d1vbka2	Alpha and beta proteins (a+b)	THUMP domain	THUMP domain-like	THUMP domain	Hypothetical protein PH1313, N-terminal domain	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d1vbkb1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	ThiI-like	Hypothetical protein PH1313, C-terminal domain	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d1vbkb2	Alpha and beta proteins (a+b)	THUMP domain	THUMP domain-like	THUMP domain	Hypothetical protein PH1313, N-terminal domain	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	ThiI-like	8020744	4002568	SCOP2 (2022-06-29)
A	SCOP2 Family	THUMP domain	8020745	4003734	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Adenine nucleotide alpha hydrolases-like	8033124	3001593	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	THUMP domain-like	8033125	3001379	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8033124	3001593	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	THUMP domain-like	8033125	3001379	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		e1vbkA1	A: Alpha-beta plaits	X: Ferredoxin-like domain in ThiI	H: Ferredoxin-like domain in ThiI	T: ThiI_fer	F:	ECOD (20:10:01)
A		e1vbkA2	A: THUMP domain-like	X: THUMP domain-like	H: THUMP domain-like	T: THUMP	F:	ECOD (20:10:01)
A		e1vbkA3	A: Flavodoxin-like	X: HAD domain-related	H: HAD-like	T:	F:	ECOD (20:10:01)
B		e1vbkB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
B		e1vbkB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
B		e1vbkB3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: SNO, Peptidase_S51	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.1510	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	THUMP domain-like	CATH (4.3.0)
A	3.30.2300.10	Alpha Beta	2-Layer Sandwich	THUMP fold	THUMP superfamily	CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	3.30.70.1510	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	THUMP domain-like	CATH (4.3.0)
B	3.30.2300.10	Alpha Beta	2-Layer Sandwich	THUMP fold	THUMP superfamily	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	hypothetical protein PH1313	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 cytidylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity nucleotidyltransferase activity catalytic activity CCA tRNA nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA binding nucleic acid binding	tRNA thio-modification tRNA 4-thiouridine biosynthesis tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA thio-modification tRNA 4-thiouridine biosynthesis tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process macromolecule metabolic process RNA processing sulfur compound biosynthetic process thiazole biosynthetic process sulfur compound metabolic process thiazole metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR020536	Thil, AANH domain	Domain
A, B	IPR004114	THUMP domain	Domain
A, B	IPR054173	ThiI, ferredoxin-like domain	Domain
A, B	IPR049962	ThiI, THUMP domain	Domain
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B	IPR050102	tRNA sulfurtransferase, ThiI	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.