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DNA_polymerase

Euk-Vir

Only_Syngen_Nebraska_virus_5

DNA_polymerase__YP_009325633__Only_Syngen_Nebraska_virus_5__1917232

Identity

Accession:
YP_009325633 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

75.5 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Algavirales› Phycodnaviridae› Chlorovirus› Only_Syngen_Nebraska_virus_5

TaxID: 1917232

Cluster

View cluster (158 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 3-173
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 34.6 2.00e-08 31.6% 21.5%
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3iayA01 2.40.50.730 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.80 39.0 5.27e-01 100.0% 84.7%
1jb7A02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.76 34.0 4.13e-01 100.0% 62.9%
2vqeL00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.71 33.0 3.80e-01 100.0% 58.9%
1fguB02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.71 36.0 4.18e-01 100.0% 67.7%
6gdxA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 39.0 4.77e-01 75.4% 88.8%
2j5aA00 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.65 40.0 4.91e-01 93.6% 97.2%
1p1lA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 36.0 4.48e-01 81.9% 89.2%
5odnC00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.65 35.0 4.51e-01 100.0% 89.2%
2yq1C00 3.30.70.390 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Epstein Barr virus nuclear antigen-1, DNA-binding domain 0.64 37.0 4.17e-01 88.3% 73.3%
4e98C00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 36.0 4.45e-01 82.5% 88.6%
3ahpA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 36.0 4.49e-01 84.8% 89.6%
4iyqA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 36.0 4.43e-01 80.7% 88.8%
5d4nC00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 35.0 4.48e-01 75.4% 93.9%
1o51A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 34.0 4.53e-01 83.6% 100.0%
2ypyA00 3.30.70.390 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Epstein Barr virus nuclear antigen-1, DNA-binding domain 0.63 37.0 4.13e-01 87.7% 73.1%
2qrrA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.61 32.0 4.07e-01 93.0% 87.6%
2apoA03 3.30.70.3190 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 33.0 4.28e-01 70.2% 97.8%
2rilA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 34.0 4.39e-01 73.7% 100.0%
3kg0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 34.0 4.27e-01 91.8% 100.0%
2qycA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 34.0 4.32e-01 84.8% 100.0%
2ftrA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 34.0 4.25e-01 91.8% 100.0%
2bbeA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 34.0 4.19e-01 98.2% 100.0%
1iujA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 33.0 4.16e-01 73.7% 100.0%
1sqeA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 32.0 4.04e-01 86.0% 98.0%
1x7vA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 32.0 4.01e-01 93.0% 100.0%
1rjjA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 34.0 4.10e-01 95.3% 98.2%
3bguA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 31.0 3.94e-01 84.2% 100.0%
5ixuA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 32.0 4.02e-01 73.7% 100.0%
1lq9A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 33.0 3.97e-01 75.4% 94.6%
3kkfA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 32.0 3.90e-01 86.5% 97.1%
2mq8A00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.52 33.0 3.99e-01 80.7% 96.4%
3fmbA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 31.0 3.91e-01 84.2% 100.0%
1r89A03 3.30.70.590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Poly(A) polymerase predicted RNA binding domain 0.52 36.0 4.03e-01 85.4% 91.0%
1r6yA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 31.0 3.90e-01 74.9% 100.0%
1f9cA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 34.0 3.97e-01 90.1% 95.1%
3ik4B01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.50 32.0 3.74e-01 98.8% 91.5%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3788812 304.114.1.6 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain › DNA_pol_B_exo1 0.87 83.0 7.27e-01 100.0% 71.7%
3800859 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.85 81.0 7.61e-01 98.8% 99.0%
3794217 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.85 81.0 5.50e-01 98.8% 42.1%
3192875 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.85 82.0 5.70e-01 100.0% 37.3%
4997715 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.85 76.0 7.69e-01 100.0% 93.5%
5054032 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.85 68.0 5.14e-01 100.0% 38.4%
3741555 4969.1.1.0 ↗ alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I 0.85 68.0 6.03e-01 82.5% 77.0%
4972474 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.84 77.0 4.96e-01 100.0% 24.1%
5023017 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.84 73.0 6.69e-01 99.4% 72.6%
4944520 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.83 77.0 6.85e-01 99.4% 71.7%
4649118 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.83 64.0 4.69e-01 78.4% 95.7%
5048995 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 73.0 5.47e-01 100.0% 41.6%
4299557 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.83 74.0 7.09e-01 98.8% 82.6%
3166912 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.82 62.0 5.99e-01 77.8% 94.7%
3508573 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.82 35.0 4.53e-01 100.0% 67.6%
3936025 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.81 44.0 5.81e-01 100.0% 93.0%
5019480 304.48.1.3 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.80 77.0 4.87e-01 100.0% 24.8%
3393168 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.78 36.0 4.52e-01 100.0% 69.1%
3705696 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.78 75.0 6.64e-01 100.0% 78.7%
3492348 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.78 38.0 4.10e-01 100.0% 54.5%
3802227 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.78 75.0 4.60e-01 100.0% 22.0%
3605750 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.78 74.0 4.54e-01 100.0% 20.3%
4405678 304.114.1.6 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain › DNA_pol_B_exo1 0.78 74.0 6.27e-01 100.0% 76.2%
None — 0.77 74.0 4.56e-01 100.0% 23.1%
4448420 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.77 73.0 6.43e-01 100.0% 76.2%
3800763 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.77 73.0 6.11e-01 100.0% 70.5%
3266685 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.77 73.0 4.31e-01 100.0% 15.1%
5030410 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.73 36.0 4.75e-01 100.0% 85.3%
5017082 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.72 63.0 4.82e-01 91.2% 69.3%
5076410 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.72 62.0 4.71e-01 90.1% 61.4%
3666655 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.71 39.0 4.50e-01 100.0% 72.8%
4502019 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.71 63.0 4.59e-01 92.4% 67.7%
3488149 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.71 36.0 4.98e-01 70.2% 98.8%
5081878 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.70 61.0 4.62e-01 90.6% 61.4%
4982481 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.70 34.0 4.56e-01 100.0% 85.3%
3474148 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.69 35.0 4.18e-01 100.0% 70.0%
5069333 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.68 59.0 4.43e-01 90.6% 59.5%
4944847 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.67 38.0 4.68e-01 91.2% 88.5%
4140821 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.67 37.0 4.59e-01 89.5% 86.7%
4957224 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.67 36.0 4.57e-01 90.1% 89.0%
5015958 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.66 37.0 4.59e-01 89.5% 88.5%
3744913 304.8.1.15 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › TH_ACT 0.66 37.0 4.69e-01 92.4% 95.8%
4167213 304.12.1.1 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › Ribosomal_S6 0.65 39.0 4.91e-01 88.3% 100.0%
4928840 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.65 36.0 4.52e-01 77.2% 91.0%
3664706 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.64 33.0 4.62e-01 73.1% 100.0%
3177336 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.62 37.0 4.54e-01 91.8% 95.2%
4938292 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.62 35.0 4.60e-01 83.6% 100.0%
3479702 304.44.1.0 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 0.61 34.0 4.24e-01 86.0% 87.6%
3941701 304.28.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › ACR_tran 0.60 36.0 4.51e-01 73.7% 97.1%
4928686 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.59 32.0 4.23e-01 71.3% 98.9%
5047792 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.59 35.0 4.27e-01 94.2% 94.3%
4031950 304.4.1.73 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › DUF4865 0.58 33.0 4.11e-01 85.4% 90.5%
4865069 304.4.1.14 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Dabb 0.58 35.0 4.41e-01 74.3% 100.0%
3915011 389.1.1.7 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin › EGF_CA 0.58 39.0 4.06e-01 90.1% 72.5%
3971521 304.28.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › ACR_tran 0.57 35.0 4.32e-01 75.4% 98.1%
3252847 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.57 29.0 3.82e-01 98.8% 94.1%
3953369 304.4.1.2 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › MIase 0.56 34.0 4.06e-01 86.0% 93.6%
3437421 304.4.1.14 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Dabb 0.55 34.0 3.91e-01 87.1% 85.8%
1933419 304.4.1.4 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.53 35.0 3.99e-01 86.0% 89.1%
3967987 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.51 32.0 3.86e-01 97.7% 98.2%
D2 high residues 183-407
PDB
Domain cluster: rep: B-family_DNA_polymerase__YP_009507574__Heterosigma_akashiwo_virus_01__97195__D190-438
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 140.5 8.60e-41 78.2% 73.1%
D3 medium residues 408-459_533-602
PDB
Domain cluster: rep: DNA_polymerase_delta_catalytic_subunit__YP_004347308__Lausannevirus__999883__D495-518_554-567_621-704
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 49.6 3.70e-13 57.4% 13.2%
D4 medium residues 460-532_603-706
PDB
Domain cluster: rep: NC_004735.1__NP_835679.1__Rm378p092__00092__D1-33_185-289
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 46.2 4.10e-12 52.5% 20.3%
PF00136.27 DNA_pol_B 60.5 1.90e-16 40.7% 11.0%