4DSE
Ternary complex of Bacillus DNA Polymerase I Large Fragment F710Y, DNA duplex, and rCTP (paired with dG of template) in presence of Mg2+
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d4dsea1 | Alpha and beta proteins (a/b) | Ribonuclease H-like motif | Ribonuclease H-like | automated matches | automated matches | (Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ], | SCOPe (2.08) |
A | d4dsea2 | Multi-domain proteins (alpha and beta) | DNA/RNA polymerases | DNA/RNA polymerases | DNA polymerase I | automated matches | (Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ], | SCOPe (2.08) |
B [auth D] | d4dsed1 | Alpha and beta proteins (a/b) | Ribonuclease H-like motif | Ribonuclease H-like | automated matches | automated matches | (Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ], | SCOPe (2.08) |
B [auth D] | d4dsed2 | Multi-domain proteins (alpha and beta) | DNA/RNA polymerases | DNA/RNA polymerases | DNA polymerase I | automated matches | (Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Ribonuclease H-like | 8042336 | 3000143 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8042337 | 3001272 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8042337 | 3001272 | SCOP2B (2022-06-29) |
B [auth D] | SCOP2B Superfamily | Ribonuclease H-like | 8042336 | 3000143 | SCOP2B (2022-06-29) |
B [auth D] | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8042337 | 3001272 | SCOP2B (2022-06-29) |
B [auth D] | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8042337 | 3001272 | 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) |
---|---|---|---|---|---|---|---|---|
A | DNA_pol_A_2nd | e4dseA3 | A: alpha arrays | X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology) | H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology) | T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I | F: DNA_pol_A_2nd | ECOD (1.6) |
A | DNA_pol_A_1st | e4dseA2 | 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: DNA_pol_A_1st | ECOD (1.6) |
A | DNA_pol_A_3rd | e4dseA5 | 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_A_3rd | ECOD (1.6) |
A | DNA_pol_A_exo1_1 | e4dseA4 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: DNA_pol_A_exo1_1 | ECOD (1.6) |
B [auth D] | DNA_pol_A_2nd | e4dseD11 | A: alpha arrays | X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology) | H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology) | T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I | F: DNA_pol_A_2nd | ECOD (1.6) |
B [auth D] | DNA_pol_A_1st | e4dseD12 | 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: DNA_pol_A_1st | ECOD (1.6) |
B [auth D] | DNA_pol_A_3rd | e4dseD9 | 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_A_3rd | ECOD (1.6) |
B [auth D] | DNA_pol_A_exo1_1 | e4dseD10 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: DNA_pol_A_exo1_1 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.30.420.10 | Alpha Beta | 2-Layer Sandwich | Nucleotidyltransferase | domain 5 | CATH (4.3.0) |
A | 1.20.1060.10 | Mainly Alpha | Up-down Bundle | Taq DNA Polymerase | Chain T, domain 4 | CATH (4.3.0) |
A | 3.30.70.370 | Alpha Beta | 2-Layer Sandwich | Alpha-Beta Plaits | CATH (4.3.0) | |
A | 1.10.150.20 | Mainly Alpha | Orthogonal Bundle | DNA polymerase | domain 1 | CATH (4.3.0) |
B [auth D] | 3.30.420.10 | Alpha Beta | 2-Layer Sandwich | Nucleotidyltransferase | domain 5 | CATH (4.3.0) |
B [auth D] | 1.20.1060.10 | Mainly Alpha | Up-down Bundle | Taq DNA Polymerase | Chain T, domain 4 | CATH (4.3.0) |
B [auth D] | 3.30.70.370 | Alpha Beta | 2-Layer Sandwich | Alpha-Beta Plaits | CATH (4.3.0) | |
B [auth D] | 1.10.150.20 | Mainly Alpha | Orthogonal Bundle | DNA polymerase | domain 1 | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A, B [auth D] | PF22619 | DNA polymerase I, ribonuclease H-like domain (DNA_polI_exo1) | DNA polymerase I, ribonuclease H-like domain | This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other related enzymes. It is one of the constituent domains of Klenow fragment. | Domain |
A, B [auth D] | PF00476 | DNA polymerase family A (DNA_pol_A) | DNA polymerase family A | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
A, B [auth D] | IPR036397 | Ribonuclease H superfamily | Homologous Superfamily |
A, B [auth D] | IPR002421 | 5'-3' exonuclease | Domain |
A, B [auth D] | IPR043502 | DNA/RNA polymerase superfamily | Homologous Superfamily |
A, B [auth D] | IPR020045 | DNA polymerase I-like, H3TH domain | Domain |
A, B [auth D] | IPR001098 | DNA-directed DNA polymerase, family A, palm domain | Domain |
A, B [auth D] | IPR029060 | PIN-like domain superfamily | Homologous Superfamily |
A, B [auth D] | IPR036279 | 5'-3' exonuclease, C-terminal domain superfamily | Homologous Superfamily |
A, B [auth D] | IPR008918 | Helix-hairpin-helix motif, class 2 | Conserved Site |
A, B [auth D] | IPR002298 | DNA polymerase A | Family |
A, B [auth D] | IPR020046 | 5'-3' exonuclease, alpha-helical arch, N-terminal | Domain |
A, B [auth D] | IPR019760 | DNA-directed DNA polymerase, family A, conserved site | Conserved Site |
A, B [auth D] | IPR018320 | DNA polymerase 1 | Family |
A, B [auth D] | IPR012337 | Ribonuclease H-like superfamily | Homologous Superfamily |
A, B [auth D] | IPR002562 | 3'-5' exonuclease domain | Domain |