3KD5
Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid.
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
C [auth E] | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8033949 | 3001272 | SCOP2B (2022-06-29) |
C [auth E] | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8033949 | 3001272 | SCOP2B (2022-06-29) |
C [auth E] | SCOP2B Superfamily | Ribonuclease H-like | 8033947 | 3000143 | 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) |
---|---|---|---|---|---|---|---|---|
C [auth E] | 43_2nd | e3kd5E5 | 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: 43_2nd | ECOD (1.6) |
C [auth E] | 43_1st | e3kd5E6 | 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: 43_1st | ECOD (1.6) |
C [auth E] | DNA_pol_B_1st | e3kd5E7 | 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 | ECOD (1.6) |
C [auth E] | DNA_pol_B_exo1_3rd | e3kd5E4 | 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) |
---|---|---|---|---|---|---|
C [auth E] | 3.30.342.10 | Alpha Beta | 2-Layer Sandwich | DNA Polymerase | Chain A, domain 1 | CATH (4.3.0) |
C [auth E] | 3.30.420.10 | Alpha Beta | 2-Layer Sandwich | Nucleotidyltransferase | domain 5 | CATH (4.3.0) |
C [auth E] | 3.90.1600.10 | Alpha Beta | Alpha-Beta Complex | Palm domain of DNA polymerase | B family DNA polymerase, palm domain | CATH (4.3.0) |
C [auth E] | 1.10.287.690 | Mainly Alpha | Orthogonal Bundle | Helix Hairpins | B family DNA polymerase, finger domain | CATH (4.3.0) |
C [auth E] | 1.20.1280.300 | Mainly Alpha | Up-down Bundle | Monooxygenase | CATH (4.3.0) | |
C [auth E] | 3.40.1820.10 | Alpha Beta | 3-Layer(aba) Sandwich | Ribonuclease H-like motif | DnaQ-like 3'-5' exonuclease | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
C [auth E] | PF03104 | DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1) | DNA polymerase family B, exonuclease domain | - | Family |
C [auth E] | PF00136 | DNA polymerase family B (DNA_pol_B) | DNA polymerase family B | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
C [auth E] | IPR036397 | Ribonuclease H superfamily | Homologous Superfamily |
C [auth E] | IPR006134 | DNA-directed DNA polymerase, family B, multifunctional domain | Domain |
C [auth E] | IPR034749 | DNA-directed DNA polymerase T4 type | Family |
C [auth E] | IPR006172 | DNA-directed DNA polymerase, family B | Family |
C [auth E] | IPR043502 | DNA/RNA polymerase superfamily | Homologous Superfamily |
C [auth E] | IPR006133 | DNA-directed DNA polymerase, family B, exonuclease domain | Domain |
C [auth E] | IPR050240 | DNA polymerase type-B | Family |
C [auth E] | IPR017964 | DNA-directed DNA polymerase, family B, conserved site | Conserved Site |
C [auth E] | IPR012337 | Ribonuclease H-like superfamily | Homologous Superfamily |
C [auth E] | IPR023211 | DNA polymerase, palm domain superfamily | Homologous Superfamily |