3A2F
Crystal Structure of Pyrococcus furiosus DNA polymerase/PCNA monomer mutant complex
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | d3a2fb1 | Alpha and beta proteins (a+b) | DNA clamp | DNA clamp | DNA polymerase processivity factor | Proliferating cell nuclear antigen (PCNA) | (Pyrococcus furiosus ) [TaxId: 2261 ], | SCOPe (2.08) |
A | d3a2fa1 | Alpha and beta proteins (a/b) | Ribonuclease H-like motif | Ribonuclease H-like | automated matches | automated matches | (Pyrococcus furiosus ) [TaxId: 2261 ], | SCOPe (2.08) |
A | d3a2fa2 | Multi-domain proteins (alpha and beta) | DNA/RNA polymerases | DNA/RNA polymerases | automated matches | automated matches | (Pyrococcus furiosus ) [TaxId: 2261 ], | SCOPe (2.08) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | PCNA_C | e3a2fB2 | A: a+b two layers | X: DNA clamp (From Topology) | H: DNA clamp (From Topology) | T: DNA clamp | F: PCNA_C | ECOD (1.6) |
B | PCNA_N_1 | e3a2fB1 | A: a+b two layers | X: DNA clamp (From Topology) | H: DNA clamp (From Topology) | T: DNA clamp | F: PCNA_N_1 | ECOD (1.6) |
A | pol2_like | e3a2fA3 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: pol2_like | ECOD (1.6) |
A | DNA_pol_B_2nd | e3a2fA2 | 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 | ECOD (1.6) |
A | DNA_pol_B_1st_2 | e3a2fA1 | 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_B_1st_2 | ECOD (1.6) |
A | DNA_pol_B_1st_1 | e3a2fA6 | 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 | pol2 | e3a2fA4 | 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: pol2 | ECOD (1.6) |
A | DNA_pol_B_exo1_3rd | e3a2fA5 | 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) |
---|---|---|---|---|---|---|
B | 3.70.10.10 | Alpha Beta | Box | Proliferating Cell Nuclear Antigen | CATH (4.3.0) | |
A | 3.30.342.10 | Alpha Beta | 2-Layer Sandwich | DNA Polymerase | Chain A, domain 1 | CATH (4.3.0) |
A | 3.30.420.10 | Alpha Beta | 2-Layer Sandwich | Nucleotidyltransferase | domain 5 | CATH (4.3.0) |
A | 3.90.1600.10 | Alpha Beta | Alpha-Beta Complex | Palm domain of DNA polymerase | B family DNA polymerase, palm domain | CATH (4.3.0) |
A | 1.10.287.690 | Mainly Alpha | Orthogonal Bundle | Helix Hairpins | B family DNA polymerase, finger domain | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF02747 | Proliferating cell nuclear antigen, C-terminal domain (PCNA_C) | Proliferating cell nuclear antigen, C-terminal domain | N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA. | Domain | |
PF00705 | Proliferating cell nuclear antigen, N-terminal domain (PCNA_N) | Proliferating cell nuclear antigen, N-terminal domain | N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA. | Domain | |
PF03104 | DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1) | DNA polymerase family B, exonuclease domain | - | Family | |
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 |
---|---|---|---|
IPR046938 | DNA clamp superfamily | Homologous Superfamily | |
IPR000730 | Proliferating cell nuclear antigen, PCNA | Family | |
IPR022649 | Proliferating cell nuclear antigen, PCNA, C-terminal | Domain | |
IPR022659 | Proliferating cell nuclear antigen, PCNA, conserved site | Conserved Site | |
IPR022648 | Proliferating cell nuclear antigen, PCNA, N-terminal | Domain | |
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 | |
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 |