4AHC | pdb_00004ahc

Crystal Structure of an Evolved Replicating DNA Polymerase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d4ahca1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d4ahca2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B	d4ahcb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B	d4ahcb2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4ahcA1	A: OB-fold	X: Rubredoxin-related	H: Rubredoxin-related	T: GFO_IDH_MocA	F:	ECOD (20:10:01)
B		e4ahcB1	A: OB-fold	X: Rubredoxin-related	H: Rubredoxin-related	T: GFO_IDH_MocA	F:	ECOD (20:10:01)

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)
A	1.10.132.60	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
B	3.30.342.10	Alpha Beta	2-Layer Sandwich	DNA Polymerase	Chain A, domain 1	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.90.1600.10	Alpha Beta	Alpha-Beta Complex	Palm domain of DNA polymerase	B family DNA polymerase, palm domain	CATH (4.3.0)
B	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, B	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
A, B	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, B	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 DNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound 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 DNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding hydrolase activity endonuclease activity nuclease activity	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A, B	IPR006172	DNA-directed DNA polymerase, family B	Family
A, B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A, B	IPR050240	DNA polymerase type-B	Family
A, B	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A, B	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A, B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.