2DY4 | pdb_00002dy4

Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
I [auth A]d2dy4a1 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]d2dy4a2 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]d2dy4b1 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]d2dy4b2 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]d2dy4c1 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]d2dy4c2 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)
L [auth D]d2dy4d1 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]d2dy4d2 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)
I [auth A]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 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)
J [auth B]SCOP2B SuperfamilyRibonuclease H-like 8033947 3000143 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)
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)
K [auth C]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8033949 3001272 SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
I [auth A]e2dy4A2 A: alpha bundlesX: EGF-likeH: Flavivirus capsid protein CT: Flavivirus capsid protein CF:ECOD (develop294)
I [auth A]RNase_P_Rpp14e2dy4A3 A: alpha bundlesX: EGF-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (develop294)
I [auth A]Hexokinase_2e2dy4A4 A: alpha bundlesX: HTHH: HTHT: winged helix domainF: Hexokinase_2ECOD (develop294)
J [auth B]e2dy4B2 A: alpha bundlesX: EGF-likeH: Flavivirus capsid protein CT: Flavivirus capsid protein CF:ECOD (develop294)
J [auth B]RNase_P_Rpp14e2dy4B3 A: alpha bundlesX: EGF-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (develop294)
J [auth B]Hexokinase_2e2dy4B4 A: alpha bundlesX: HTHH: HTHT: winged helix domainF: Hexokinase_2ECOD (develop294)
K [auth C]e2dy4C2 A: alpha bundlesX: EGF-likeH: Flavivirus capsid protein CT: Flavivirus capsid protein CF:ECOD (develop294)
K [auth C]RNase_P_Rpp14e2dy4C3 A: alpha bundlesX: EGF-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (develop294)
K [auth C]Hexokinase_2e2dy4C4 A: alpha bundlesX: HTHH: HTHT: winged helix domainF: Hexokinase_2ECOD (develop294)
L [auth D]e2dy4D2 A: alpha bundlesX: EGF-likeH: Flavivirus capsid protein CT: Flavivirus capsid protein CF:ECOD (develop294)
L [auth D]RNase_P_Rpp14e2dy4D3 A: alpha bundlesX: EGF-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (develop294)
L [auth D]Hexokinase_2e2dy4D4 A: alpha bundlesX: HTHH: HTHT: winged helix domainF: Hexokinase_2ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
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)
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)
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)
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)

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
I [auth A],
J [auth B],
K [auth C],
L [auth D]		DNA polymerase -
B [auth F],
D [auth H],
F [auth J],
H [auth L]		5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'---
A [auth E],
C [auth G],
E [auth I],
G [auth K]		5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-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