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DNA_polymerase

Euk-Vir

Ostreococcus_tauri_virus_2

DNA_polymerase__YP_004063640__Ostreococcus_tauri_virus_2__696472

Identity

Accession:
YP_004063640 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

84.9 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Algavirales› Phycodnaviridae› Prasinovirus› Ostreococcus_tauri_virus_2

TaxID: 696472

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 2-182
PDB
Domain cluster: rep: DNA_polymerase__YP_010084862__Shrimp_hemocyte_iridescent_virus__2039780__D2-200
D2 high residues 192-411
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 123.9 1.00e-35 77.7% 73.1%
D3 medium residues 412-455_543-591
PDB
Domain cluster: rep: DNA_polymerase__YP_008052566__Phaeocystis_globosa_virus__251749__D724-746_869-928
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 39.9 3.50e-10 54.8% 11.0%
D4 medium residues 470-490_629-718
PDB
Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_002608259__Human_herpesvirus_5__10359__D703-718_902-984
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 64.2 1.40e-17 84.7% 17.9%
D5 medium residues 491-542_592-628
PDB
Domain cluster: rep: rh87__YP_068180__Macacine_betaherpesvirus_3__47929__D595-644_698-744
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 32.2 7.50e-08 58.4% 10.6%
PF00136.27 DNA_pol_B 30.2 3.00e-07 42.7% 7.5%
D6 medium residues 719-765_857-874
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3iayA07 1.10.132.60 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain 0.92 85.0 6.30e-01 100.0% 90.1%
4qclA05 1.10.132.60 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain 0.88 80.0 5.84e-01 100.0% 88.7%
1tgoA05 1.10.132.60 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain 0.84 77.0 5.60e-01 100.0% 83.8%
1o0sA02 1.20.1370.30 Mainly Alpha › Up-down Bundle › Hemocyanin, N-terminal domain › 0.74 53.0 4.47e-01 90.8% 45.4%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.69 59.0 4.96e-01 100.0% 87.1%
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 56.0 4.89e-01 93.8% 84.2%
5o5jT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.65 52.0 4.83e-01 89.2% 72.9%
6jkvA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.62 54.0 3.73e-01 100.0% 40.4%
3kd4A02 3.10.620.30 Alpha Beta › Roll › C8orf32 fold › 0.62 51.0 3.91e-01 93.8% 69.4%
1x8zB00 1.20.140.40 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Invertase/pectin methylesterase inhibitor family protein 0.62 53.0 4.20e-01 100.0% 61.2%
1go3F02 6.10.140.10 Special › Helix non-globular › Helix Hairpins › 0.61 33.0 3.76e-01 70.8% 70.2%
1xg2B00 1.20.140.40 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Invertase/pectin methylesterase inhibitor family protein 0.61 52.0 4.09e-01 100.0% 72.2%
2ebfX02 1.20.140.180 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.61 51.0 4.12e-01 100.0% 53.8%
2kobA01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.61 53.0 4.75e-01 100.0% 79.6%
4gbjC02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.60 47.0 3.81e-01 89.2% 80.7%
2hz8A00 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.60 43.0 3.60e-01 76.9% 57.4%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.58 46.0 4.45e-01 87.7% 85.3%
3qsgA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.57 44.0 3.72e-01 86.2% 77.4%
4wr4A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.56 45.0 3.95e-01 92.3% 76.2%
3u4qB04 6.10.140.1030 Special › Helix non-globular › Helix Hairpins › 0.54 39.0 3.85e-01 87.7% 73.9%
1vgpA02 1.10.230.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450-Terp; domain 2 › Cytochrome P450-Terp, domain 2 0.53 45.0 3.93e-01 98.5% 76.9%
2ibpA02 1.10.230.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450-Terp; domain 2 › Cytochrome P450-Terp, domain 2 0.53 48.0 4.04e-01 100.0% 96.2%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3167790 4969.1.1.1 ↗ 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 › DNA_pol_B 0.93 87.0 6.40e-01 100.0% 91.3%
4674133 4969.1.1.1 ↗ 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 › DNA_pol_B 0.92 86.0 6.09e-01 100.0% 87.4%
5031722 4969.1.1.1 ↗ 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 › DNA_pol_B 0.90 82.0 6.02e-01 100.0% 85.6%
4547010 4969.1.1.1 ↗ 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 › DNA_pol_B 0.89 81.0 5.75e-01 100.0% 80.0%
3705557 4969.1.1.1 ↗ 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 › DNA_pol_B 0.88 80.0 5.90e-01 100.0% 91.9%
4959102 4969.1.1.1 ↗ 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 › DNA_pol_B 0.87 80.0 5.75e-01 100.0% 82.8%
4931233 4969.1.1.1 ↗ 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 › DNA_pol_B 0.85 78.0 5.88e-01 100.0% 96.6%
5044378 4969.1.1.1 ↗ 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 › DNA_pol_B 0.83 75.0 5.67e-01 100.0% 96.0%
5046396 4969.1.1.1 ↗ 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 › DNA_pol_B 0.82 73.0 5.40e-01 100.0% 89.0%
5076363 4995.1.1.1 ↗ alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.73 59.0 5.46e-01 89.2% 76.5%
3574413 603.2.1.0 ↗ alpha bundles › STAT-like › STAT › STAT 0.72 58.0 5.25e-01 90.8% 76.7%
5012498 3843.1.1.28 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › MbhD 0.70 49.0 4.90e-01 72.3% 93.8%
4999823 4995.1.1.1 ↗ alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.70 55.0 5.24e-01 89.2% 81.2%
4323909 101.11.1.1 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.70 57.0 5.09e-01 92.3% 86.3%
5045531 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.68 56.0 5.18e-01 90.8% 81.2%
4012210 601.14.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin 0.67 57.0 4.47e-01 100.0% 75.3%
4629067 633.24.1.5 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › PF29080 0.64 51.0 4.80e-01 92.3% 91.8%
3576407 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.64 50.0 4.27e-01 89.2% 86.1%
4004067 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.64 50.0 4.64e-01 89.2% 80.0%
5044747 3236.1.1.1 ↗ alpha complex topology › Cation-proton antiporter › Cation-proton antiporter (CPA) › Cation-proton antiporter (CPA) › Na_H_Exchanger 0.63 54.0 3.31e-01 98.5% 70.8%
3704188 192.15.1.1 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › VPS28 0.62 49.0 4.40e-01 89.2% 81.1%
3669 633.16.1.1 ↗ alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like › MLD 0.61 51.0 4.60e-01 100.0% 78.6%
4298721 633.24.1.2 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › DUF5601 0.61 49.0 4.49e-01 92.3% 91.1%
3701020 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.61 48.0 4.54e-01 89.2% 87.5%
4990095 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.60 46.0 4.27e-01 83.1% 76.5%
5049361 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.60 47.0 4.49e-01 89.2% 90.0%
3815499 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.60 52.0 4.17e-01 100.0% 75.0%
3771070 627.1.1.1 ↗ alpha complex topology › VPS9 domain › VPS9 domain › VPS9 domain › VPS9 0.59 50.0 3.93e-01 100.0% 57.4%
3962601 172.1.1.0 ↗ alpha complex topology › Citrate synthase-like › Citrate synthase › Citrate synthase 0.56 49.0 2.98e-01 96.9% 25.9%
3427035 622.1.1.30 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › PF26575 0.56 46.0 4.63e-01 93.8% 100.0%
3559718 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.55 42.0 3.66e-01 87.7% 80.0%
3592539 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 43.0 3.66e-01 87.7% 56.5%
D7 medium residues 766-856
PDB
Domain cluster: rep: hypothetical_protein_PBCV1_A188aR__YP_004678908__Paramecium_bursaria_Chlorella_virus_1__10506__D2-70
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 45.1 8.80e-12 83.5% 14.8%
D8 medium residues 897-954
PDB