3K5N
Crystal structure of E.coli Pol II-abasic DNA binary complex
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d3k5na1 | Alpha and beta proteins (a/b) | Ribonuclease H-like motif | Ribonuclease H-like | DnaQ-like 3'-5' exonuclease | automated matches | (Escherichia coli ) [TaxId: 562 ], | SCOPe (2.08) |
A | d3k5na2 | Multi-domain proteins (alpha and beta) | DNA/RNA polymerases | DNA/RNA polymerases | DNA polymerase I | automated matches | (Escherichia coli ) [TaxId: 562 ], | SCOPe (2.08) |
B | d3k5nb1 | Alpha and beta proteins (a/b) | Ribonuclease H-like motif | Ribonuclease H-like | DnaQ-like 3'-5' exonuclease | automated matches | (Escherichia coli ) [TaxId: 562 ], | SCOPe (2.08) |
B | d3k5nb2 | Multi-domain proteins (alpha and beta) | DNA/RNA polymerases | DNA/RNA polymerases | DNA polymerase I | automated matches | (Escherichia coli ) [TaxId: 562 ], | SCOPe (2.08) |
B | d3k5nb3 | Artifacts | Tags | Tags | Tags | N-terminal Tags | (Escherichia coli ) [TaxId: 562 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8039908 | 3001272 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8039908 | 3001272 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Ribonuclease H-like | 8039907 | 3000143 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8039908 | 3001272 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Ribonuclease H-like | 8039907 | 3000143 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Nucleotide cyclase/DNA polymerase palm domain-like | 8039908 | 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_B_2nd_1 | e3k5nA3 | 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: DNA_pol_B_2nd_1 | ECOD (1.6) |
A | POLBc_Pol_II | e3k5nA4 | 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: POLBc_Pol_II | ECOD (1.6) |
A | DNA_pol_B_1st_1 | e3k5nA1 | 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_1 | ECOD (1.6) |
A | PRK05762_1st,DNA_pol_B_exo1_3rd | e3k5nA6 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: PRK05762_1st,DNA_pol_B_exo1_3rd | ECOD (1.6) |
B | PRK05762_1st | e3k5nB1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PRK05762_1st | ECOD (1.6) |
B | DNA_pol_B_2nd_1 | e3k5nB5 | 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: DNA_pol_B_2nd_1 | ECOD (1.6) |
B | POLBc_Pol_II | e3k5nB7 | 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: POLBc_Pol_II | ECOD (1.6) |
B | DNA_pol_B_1st_1 | e3k5nB4 | 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_1 | ECOD (1.6) |
B | PRK05762_2nd | e3k5nB3 | A: a+b two layers | X: Alpha-beta plaits | H: Family B DNA polymerase insertion domain (From Topology) | T: Family B DNA polymerase insertion domain | F: PRK05762_2nd | ECOD (1.6) |
B | DNA_pol_B_exo1_3rd | e3k5nB6 | 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
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF21474 | DNA polymerase II, N-terminal (DNApolII_N) | DNA polymerase II, N-terminal | This is the N-terminal domain of bacterial DNA polymerase II. This entry represents the OB fold [1]. | Domain | |
PF22587 | DNA polymerase II, insertion domain (DNApolII_insertion) | DNA polymerase II, insertion domain | This is the insertion domain found in DNA polymerase II from E. coli, a member of family B of DNA polymerases [1]. | Domain | |
PF00136 | DNA polymerase family B (DNA_pol_B) | DNA polymerase family B | - | Family | |
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
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR036397 | Ribonuclease H superfamily | Homologous Superfamily | |
IPR006134 | DNA-directed DNA polymerase, family B, multifunctional domain | Domain | |
IPR006172 | DNA-directed DNA polymerase, family B | Family | |
IPR043502 | DNA/RNA polymerase superfamily | Homologous Superfamily | |
IPR006133 | DNA-directed DNA polymerase, family B, exonuclease domain | Domain | |
IPR050240 | DNA polymerase type-B | Family | |
IPR042087 | DNA polymerase family B, thumb domain | Homologous Superfamily | |
IPR017964 | DNA-directed DNA polymerase, family B, conserved site | Conserved Site | |
IPR012337 | Ribonuclease H-like superfamily | Homologous Superfamily | |
IPR023211 | DNA polymerase, palm domain superfamily | Homologous Superfamily |