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DNA_polymerase

Euk-Vir

Vaccinia_virus

DNA_polymerase__YP_232947__Vaccinia_virus__10245

Identity

Accession:
YP_232947 ↗
Protein ID:
DNA_polymerase
Kingdom:
euk

Quality

84.4 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Pokkesviricetes› Chitovirales› Poxviridae› Orthopoxvirus› Orthopoxvirus_vaccinia

TaxID: 10245

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 347-432
PDB
Domain cluster: rep: DNA_polymerase_elongation_subunit_family_B__YP_009162448__Salmon_gill_poxvirus__1680908__D388-474
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08408.17 best DNA_pol_B_3 78.1 1.00e-21 96.5% 64.8%
D2 high residues 540-600_668-825
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 146.0 2.20e-42 73.5% 29.1%
PF00136.27 DNA_pol_B 48.1 1.10e-12 26.9% 10.8%
D3 medium residues 19-59_89-160
PDB
Domain cluster: rep: DNA_polymerase__YP_784249__Nile_crocodilepox_virus__1285600__D2-148
D4 medium residues 161-261
PDB
Domain cluster: rep: DNA_polymerase_elongation_subunit_family_B__YP_010088005__Lymphocystis_disease_virus_4__2704413__D159-241
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3iayA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.74 60.0 4.58e-01 100.0% 39.9%
3cetB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.69 38.0 3.70e-01 99.0% 49.1%
2p1jA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.63 50.0 4.51e-01 100.0% 61.6%
1j54A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 50.0 4.17e-01 100.0% 52.3%
4okeA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 49.0 4.20e-01 100.0% 55.6%
3sojB00 3.30.700.10 Alpha Beta › 2-Layer Sandwich › Glycoprotein, Type 4 Pilin › Glycoprotein, Type 4 Pilin 0.59 38.0 3.64e-01 84.2% 56.5%
2qkdA03 2.20.25.420 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ZPR1, zinc finger domain 0.58 29.0 3.94e-01 73.3% 96.1%
3moiA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.57 41.0 3.21e-01 74.3% 51.0%
2g1lA00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.53 34.0 3.46e-01 74.3% 65.0%
4qozB02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 48.0 3.68e-01 100.0% 45.5%
1gqyB02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.52 38.0 3.06e-01 79.2% 91.2%
4b08A01 2.40.50.730 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 37.0 4.03e-01 93.1% 92.6%
2gdqA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 33.0 3.27e-01 96.0% 61.7%
4bq6F00 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.51 45.0 3.99e-01 100.0% 75.8%
3bjsA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 33.0 3.15e-01 95.0% 56.4%
4ibnA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.50 38.0 3.10e-01 100.0% 42.6%
1tkkA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.50 35.0 3.38e-01 95.0% 63.5%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3089543 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.98 95.0 7.11e-01 100.0% 47.9%
4990754 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.84 54.0 4.05e-01 100.0% 29.3%
5076410 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 54.0 3.52e-01 100.0% 17.8%
5039400 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 54.0 3.73e-01 100.0% 22.3%
4982659 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 52.0 3.49e-01 100.0% 18.6%
4504110 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 0.82 59.0 3.80e-01 100.0% 18.1%
4939488 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.82 55.0 3.83e-01 100.0% 23.8%
5036329 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.82 50.0 3.68e-01 100.0% 26.4%
4956223 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.81 52.0 3.63e-01 100.0% 22.4%
5073475 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.81 50.0 3.45e-01 100.0% 20.3%
4988803 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.81 58.0 3.78e-01 99.0% 19.0%
5068716 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.81 53.0 3.62e-01 100.0% 21.3%
4966854 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.80 50.0 3.34e-01 100.0% 17.8%
5067181 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.80 59.0 3.80e-01 100.0% 18.6%
5029084 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.80 57.0 4.33e-01 100.0% 33.3%
4942685 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 0.79 58.0 3.60e-01 100.0% 15.7%
5027238 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.78 45.0 3.89e-01 96.0% 38.7%
5043498 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 53.0 3.44e-01 100.0% 17.9%
3705562 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.69 59.0 3.56e-01 100.0% 14.0%
3951189 2484.1.1.68 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.69 48.0 3.61e-01 100.0% 31.7%
3383138 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.67 37.0 4.16e-01 95.0% 69.2%
5017856 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 52.0 3.79e-01 100.0% 31.9%
3954042 2.1.1.94 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › TLP1_add_C 0.65 35.0 4.00e-01 94.1% 70.3%
5048191 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.65 50.0 5.10e-01 100.0% 83.0%
3287981 2.1.1.94 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › TLP1_add_C 0.63 37.0 4.17e-01 94.1% 77.3%
4298195 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.62 50.0 3.92e-01 100.0% 42.5%
4428763 2484.1.1.36 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.61 42.0 3.16e-01 100.0% 29.6%
3226038 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.57 48.0 4.01e-01 100.0% 52.8%
165020 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.56 35.0 3.24e-01 95.0% 49.2%
3248027 2003.1.5.53 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr 0.55 48.0 3.15e-01 99.0% 68.7%
4236550 2003.1.5.82 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.54 47.0 3.14e-01 98.0% 77.7%
3756825 2003.1.5.53 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr 0.53 46.0 3.08e-01 99.0% 76.1%
4943476 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 47.0 3.46e-01 99.0% 36.4%
3993235 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.52 47.0 3.70e-01 100.0% 50.2%
3741657 220.1.1.11 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rpn13_ADRM1_Pru 0.51 30.0 2.93e-01 96.0% 50.4%
3617894 9.1.1.45 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › FBO_C 0.51 40.0 3.52e-01 85.1% 96.8%
4175964 244.3.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › SufE/NifU › SufE/NifU 0.50 35.0 3.57e-01 78.2% 73.0%
D5 medium residues 829-997
PDB
Domain cluster: rep: IMGVR_UViG_3300021255_003095-3300021255-Ga0223825_1010595139__D209-342
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 117.0 1.30e-33 93.5% 32.9%