6HMS | pdb_00006hms

Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8055689	3001330	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8053389	3001067	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8053391	3000135	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)
B	MDN1_4th	e6hmsB1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: MDN1_4th	ECOD (develop294)
A	Cystatin	e6hmsA01	A: alpha bundles	X: Rossmann-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Cystatin	ECOD (develop294)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth T]	DNA (5'-D(PTPGPAPCPGPCPGPGPCPCPCPGPTPCPTPC)-3')	-	-	-
C [auth P]	DNA (5'-D(GPAPGPAPCPGPGPGPCPCPGPCPGPTP*C)-3')	-	-	-
B	DNA polymerase II large subunit,DNA polymerase II large subunit	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 DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity 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 DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity	catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process intein-mediated protein splicing gene expression catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process intein-mediated protein splicing gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing protein metabolic process protein splicing DNA-templated DNA replication DNA replication	-
A	DNA polymerase II small subunit	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 DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity 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 DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity	catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation DNA replication DNA strand elongation involved in DNA replication	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR016033	DNA polymerase II large subunit DP2, N-terminal	Domain
B	IPR036844	Hint domain superfamily	Homologous Superfamily
B	IPR030934	Intein C-terminal splicing region	Conserved Site
B	IPR006141	Intein N-terminal splicing region	PTM
B	IPR056171	DNA polymerase II large subunit DP2, central domain	Domain
B	IPR056172	DNA polymerase II large subunit DP2, catalytic domain	Domain
B	IPR003587	Hint domain N-terminal	Domain
B	IPR004475	DNA polymerase II large subunit DP2	Family
A	IPR054750	DNA polymerase II small subunit, N-terminal domain	Domain
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR011149	DNA polymerase II small subunit, archaeal	Family
A	IPR024826	DNA polymerase delta/II small subunit family	Family
A	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
A	IPR029052	Metallo-dependent phosphatase-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.