2XHB

Crystal structure of DNA polymerase from Thermococcus gorgonarius in complex with hypoxanthine-containing DNA

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	d2xhba1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	automated matches	(Thermococcus gorgonarius ) [TaxId: 71997 ],	SCOPe (2.08)
A	d2xhba2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	automated matches	(Thermococcus gorgonarius ) [TaxId: 71997 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribonuclease H-like	8044544	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037444	3001272	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	pol2_like	e2xhbA6	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: pol2_like	ECOD (1.6)
A	DNA_pol_B_2nd	e2xhbA5	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: DNA_pol_B_2nd	ECOD (1.6)
A	DNA_pol_B_1st_2	e2xhbA3	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: DNA_pol_B_1st_2	ECOD (1.6)
A	DNA_pol_B_1st_1	e2xhbA4	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: DNA_pol_B_1st_1	ECOD (1.6)
A	pol2	e2xhbA2	A: a+b two layers	X: Alpha-beta plaits	H: Family B DNA polymerase insertion domain (From Topology)	T: Family B DNA polymerase insertion domain	F: pol2	ECOD (1.6)
A	DNA_pol_B_exo1_3rd	e2xhbA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_B_exo1_3rd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.90.1600.10	Alpha Beta	Alpha-Beta Complex	Palm domain of DNA polymerase	B family DNA polymerase, palm domain	CATH (4.3.0)
A	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
A	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA POLYMERASE	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups nuclease activity hydrolase activity, acting on ester bonds hydrolase activity exonuclease activity DNA binding binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups nuclease activity hydrolase activity, acting on ester bonds hydrolase activity exonuclease activity DNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	-
B [auth D]	HYPOXANTHINE-CONTAINING DNA	-	-	-
C [auth E]	5'-D(APAPAPAPAPAPAPAP*A)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A	IPR006172	DNA-directed DNA polymerase, family B	Family
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR050240	DNA polymerase type-B	Family
A	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR023211	DNA polymerase, palm domain superfamily	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.