1Q9X | pdb_00001q9x

Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA

External Resource: Annotation


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
L [auth D]d1q9xd1 Alpha and beta proteins (a/b) Ribonuclease H-like motif Ribonuclease H-like DnaQ-like 3'-5' exonuclease Exonuclease domain of family B DNA polymerases (Escherichia phage RB69 ) [TaxId: 12353 ], SCOPe (2.08)
L [auth D]d1q9xd2 Multi-domain proteins (alpha and beta) DNA/RNA polymerases DNA/RNA polymerases DNA polymerase I Family B DNA polymerase (Escherichia phage RB69 ) [TaxId: 12353 ], SCOPe (2.08)
K [auth C]d1q9xc1 Alpha and beta proteins (a/b) Ribonuclease H-like motif Ribonuclease H-like DnaQ-like 3'-5' exonuclease Exonuclease domain of family B DNA polymerases (Escherichia phage RB69 ) [TaxId: 12353 ], SCOPe (2.08)
K [auth C]d1q9xc2 Multi-domain proteins (alpha and beta) DNA/RNA polymerases DNA/RNA polymerases DNA polymerase I Family B DNA polymerase (Escherichia phage RB69 ) [TaxId: 12353 ], SCOPe (2.08)
J [auth B]d1q9xb1 Alpha and beta proteins (a/b) Ribonuclease H-like motif Ribonuclease H-like DnaQ-like 3'-5' exonuclease Exonuclease domain of family B DNA polymerases (Escherichia phage RB69 ) [TaxId: 12353 ], SCOPe (2.08)
J [auth B]d1q9xb2 Multi-domain proteins (alpha and beta) DNA/RNA polymerases DNA/RNA polymerases DNA polymerase I Family B DNA polymerase (Escherichia phage RB69 ) [TaxId: 12353 ], SCOPe (2.08)
I [auth A]d1q9xa1 Alpha and beta proteins (a/b) Ribonuclease H-like motif Ribonuclease H-like DnaQ-like 3'-5' exonuclease Exonuclease domain of family B DNA polymerases (Escherichia phage RB69 ) [TaxId: 12353 ], SCOPe (2.08)
I [auth A]d1q9xa2 Multi-domain proteins (alpha and beta) DNA/RNA polymerases DNA/RNA polymerases DNA polymerase I Family B DNA polymerase (Escherichia phage RB69 ) [TaxId: 12353 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
L [auth D]SCOP2B SuperfamilyRibonuclease H-like 8033947 3000143 SCOP2B (2022-06-29)
L [auth D]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 SCOP2B (2022-06-29)
L [auth D]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 SCOP2B (2022-06-29)
K [auth C]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 SCOP2B (2022-06-29)
K [auth C]SCOP2B SuperfamilyRibonuclease H-like 8033947 3000143 SCOP2B (2022-06-29)
K [auth C]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 SCOP2B (2022-06-29)
J [auth B]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 SCOP2B (2022-06-29)
J [auth B]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 SCOP2B (2022-06-29)
J [auth B]SCOP2B SuperfamilyRibonuclease H-like 8033947 3000143 SCOP2B (2022-06-29)
I [auth A]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 SCOP2B (2022-06-29)
I [auth A]SCOP2B SuperfamilyRibonuclease H-like 8033947 3000143 SCOP2B (2022-06-29)
I [auth A]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
L [auth D]e1q9xD2 A: alpha bundlesX: EGF-likeH: Flavivirus capsid protein CT: Flavivirus capsid protein CF:ECOD (develop294)
L [auth D]RNase_P_Rpp14e1q9xD3 A: alpha bundlesX: EGF-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (develop294)
L [auth D]Hexokinase_2e1q9xD4 A: alpha bundlesX: HTHH: HTHT: winged helix domainF: Hexokinase_2ECOD (develop294)
K [auth C]e1q9xC2 A: alpha bundlesX: EGF-likeH: Flavivirus capsid protein CT: Flavivirus capsid protein CF:ECOD (develop294)
K [auth C]RNase_P_Rpp14e1q9xC3 A: alpha bundlesX: EGF-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (develop294)
K [auth C]Hexokinase_2e1q9xC4 A: alpha bundlesX: HTHH: HTHT: winged helix domainF: Hexokinase_2ECOD (develop294)
J [auth B]e1q9xB2 A: alpha bundlesX: EGF-likeH: Flavivirus capsid protein CT: Flavivirus capsid protein CF:ECOD (develop294)
J [auth B]RNase_P_Rpp14e1q9xB3 A: alpha bundlesX: EGF-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (develop294)
J [auth B]Hexokinase_2e1q9xB4 A: alpha bundlesX: HTHH: HTHT: winged helix domainF: Hexokinase_2ECOD (develop294)
I [auth A]e1q9xA2 A: alpha bundlesX: EGF-likeH: Flavivirus capsid protein CT: Flavivirus capsid protein CF:ECOD (develop294)
I [auth A]RNase_P_Rpp14e1q9xA3 A: alpha bundlesX: EGF-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (develop294)
I [auth A]Hexokinase_2e1q9xA4 A: alpha bundlesX: HTHH: HTHT: winged helix domainF: Hexokinase_2ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
L [auth D]3.30.342.10 Alpha Beta 2-Layer Sandwich DNA Polymerase Chain A, domain 1CATH (4.3.0)
L [auth D]3.30.420.10 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5CATH (4.3.0)
L [auth D]3.90.1600.10 Alpha Beta Alpha-Beta Complex Palm domain of DNA polymerase B family DNA polymerase, palm domainCATH (4.3.0)
L [auth D]1.10.287.690 Mainly Alpha Orthogonal Bundle Helix Hairpins B family DNA polymerase, finger domainCATH (4.3.0)
L [auth D]1.20.1280.300 Mainly Alpha Up-down Bundle Monooxygenase CATH (4.3.0)
L [auth D]3.40.1820.10 Alpha Beta 3-Layer(aba) Sandwich Ribonuclease H-like motif DnaQ-like 3'-5' exonucleaseCATH (4.3.0)
K [auth C]3.30.342.10 Alpha Beta 2-Layer Sandwich DNA Polymerase Chain A, domain 1CATH (4.3.0)
K [auth C]3.30.420.10 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5CATH (4.3.0)
K [auth C]3.90.1600.10 Alpha Beta Alpha-Beta Complex Palm domain of DNA polymerase B family DNA polymerase, palm domainCATH (4.3.0)
K [auth C]1.10.287.690 Mainly Alpha Orthogonal Bundle Helix Hairpins B family DNA polymerase, finger domainCATH (4.3.0)
K [auth C]1.20.1280.300 Mainly Alpha Up-down Bundle Monooxygenase CATH (4.3.0)
K [auth C]3.40.1820.10 Alpha Beta 3-Layer(aba) Sandwich Ribonuclease H-like motif DnaQ-like 3'-5' exonucleaseCATH (4.3.0)
J [auth B]3.30.342.10 Alpha Beta 2-Layer Sandwich DNA Polymerase Chain A, domain 1CATH (4.3.0)
J [auth B]3.30.420.10 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5CATH (4.3.0)
J [auth B]3.90.1600.10 Alpha Beta Alpha-Beta Complex Palm domain of DNA polymerase B family DNA polymerase, palm domainCATH (4.3.0)
J [auth B]1.10.287.690 Mainly Alpha Orthogonal Bundle Helix Hairpins B family DNA polymerase, finger domainCATH (4.3.0)
J [auth B]1.20.1280.300 Mainly Alpha Up-down Bundle Monooxygenase CATH (4.3.0)
J [auth B]3.40.1820.10 Alpha Beta 3-Layer(aba) Sandwich Ribonuclease H-like motif DnaQ-like 3'-5' exonucleaseCATH (4.3.0)
I [auth A]3.30.342.10 Alpha Beta 2-Layer Sandwich DNA Polymerase Chain A, domain 1CATH (4.3.0)
I [auth A]3.30.420.10 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5CATH (4.3.0)
I [auth A]3.90.1600.10 Alpha Beta Alpha-Beta Complex Palm domain of DNA polymerase B family DNA polymerase, palm domainCATH (4.3.0)
I [auth A]1.10.287.690 Mainly Alpha Orthogonal Bundle Helix Hairpins B family DNA polymerase, finger domainCATH (4.3.0)
I [auth A]1.20.1280.300 Mainly Alpha Up-down Bundle Monooxygenase CATH (4.3.0)
I [auth A]3.40.1820.10 Alpha Beta 3-Layer(aba) Sandwich Ribonuclease H-like motif DnaQ-like 3'-5' exonucleaseCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth A],
J [auth B],
K [auth C],
L [auth D]		PF03104DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)DNA polymerase family B, exonuclease domain- Family
I [auth A],
J [auth B],
K [auth C],
L [auth D]		PF00136DNA polymerase family B (DNA_pol_B)DNA polymerase family B- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B [auth I],
D [auth J],
F [auth K],
H [auth L]		5'-AC(tetrahydrofuran)GGTAAGCAGTCCGCGG-3'---
I [auth A],
J [auth B],
K [auth C],
L [auth D]		DNA polymerase -
A [auth E],
C [auth F],
E [auth G],
G [auth H]		5'-GCGGACTGCTTAC(dideoxycytidine)-3'---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR036397Ribonuclease H superfamilyHomologous Superfamily
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR006134DNA-directed DNA polymerase, family B, multifunctional domainDomain
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR034749DNA-directed DNA polymerase T4 typeFamily
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR006172DNA-directed DNA polymerase, family BFamily
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR006133DNA-directed DNA polymerase, family B, exonuclease domainDomain
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR050240DNA polymerase type-BFamily
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR017964DNA-directed DNA polymerase, family B, conserved siteConserved Site
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
I [auth A],
J [auth B],
K [auth C],
L [auth D]		IPR023211DNA polymerase, palm domain superfamilyHomologous Superfamily