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DNA_polymerase-beta_AP_pol

Euk-Vir

Choristoneura_biennis_entomopoxvirus

DNA_polymerase-beta_AP_pol__YP_008004307__Choristoneura_biennis_entomopoxvirus__10288

Identity

Accession:
YP_008004307 ↗
Protein ID:
DNA_polymerase-beta_AP_pol
Kingdom:
euk

Quality

70.6 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Pokkesviricetes› Chitovirales› Poxviridae› Betaentomopoxvirus› Choristoneura_biennis_entomopoxvirus

TaxID: 10288

Cluster

View cluster (5 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 11-275
PDB
D2 medium residues 292-385
PDB
Domain cluster: rep: putative_DNA_polymerase_X_family_protein__YP_009052122__Aureococcus_anophagefferens_virus__1474867__D1-77
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hx0K01 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.84 66.0 7.03e-01 97.9% 92.8%
6h5hA00 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.82 60.0 6.81e-01 92.6% 100.0%
3b0xA01 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.78 68.0 7.04e-01 100.0% 98.9%
2kp7A01 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.78 59.0 6.54e-01 96.8% 100.0%
2fiyA00 3.90.1670.10 Alpha Beta › Alpha-Beta Complex › FdhE-like fold › FdhE-like domain 0.70 60.0 4.27e-01 94.7% 87.4%
3p42A02 6.10.250.2280 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.69 42.0 4.86e-01 90.4% 82.9%
2qffA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.64 41.0 4.53e-01 84.0% 81.1%
2pejA00 1.10.1200.210 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Chaperonin-like RbcX 0.64 46.0 4.38e-01 98.9% 64.2%
3c8tA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.63 47.0 4.72e-01 93.6% 77.3%
3lcnB00 1.10.340.40 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain 0.62 52.0 5.24e-01 100.0% 88.7%
1lkoA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.62 48.0 4.15e-01 81.9% 82.8%
4gr6B00 1.10.1200.210 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Chaperonin-like RbcX 0.62 39.0 3.78e-01 95.7% 56.2%
2felA00 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.60 52.0 3.61e-01 100.0% 58.2%
1a87A02 1.10.490.30 Mainly Alpha › Orthogonal Bundle › Globin-like › Colicin 0.59 45.0 3.56e-01 96.8% 38.0%
2nobA03 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.58 48.0 4.38e-01 90.4% 99.2%
2h56A02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.58 49.0 4.61e-01 92.6% 99.1%
1vsgA01 3.90.150.10 Alpha Beta › Alpha-Beta Complex › Variant Surface Glycoprotein; Chain A domain 1 › Variant Surface Glycoprotein, subunit A domain 1 0.57 45.0 3.51e-01 84.0% 92.1%
4gr2A00 1.10.1200.210 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Chaperonin-like RbcX 0.57 39.0 3.74e-01 95.7% 60.0%
6umqA01 1.20.930.60 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.56 42.0 4.00e-01 80.9% 91.3%
4n06A02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.55 51.0 3.62e-01 98.9% 76.5%
7p5hB03 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.55 44.0 4.53e-01 90.4% 89.9%
6mh4A03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.54 34.0 3.70e-01 94.7% 74.7%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.54 38.0 3.87e-01 84.0% 74.7%
5figA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.54 46.0 4.50e-01 90.4% 88.0%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.54 35.0 3.66e-01 85.1% 70.5%
1t6jA03 1.10.274.20 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Phenylalanine ammonia-lyase 1; domain 3 0.54 45.0 4.46e-01 95.7% 88.3%
3kavA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.54 46.0 4.47e-01 90.4% 97.1%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.53 40.0 4.29e-01 87.2% 96.2%
4yosA02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.53 39.0 3.32e-01 78.7% 95.0%
3vkgA09 1.20.920.30 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.53 40.0 3.55e-01 83.0% 93.1%
2lyiA01 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.52 43.0 3.81e-01 93.6% 97.3%
1aepA00 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.52 42.0 3.69e-01 92.6% 64.7%
2k3oA00 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.52 44.0 4.03e-01 98.9% 70.5%
4unfA02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.51 45.0 4.21e-01 100.0% 89.7%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.51 34.0 3.57e-01 84.0% 75.3%
2hg2A01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.50 36.0 2.67e-01 77.7% 79.4%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3178379 102.1.1.30 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HHH_8 0.86 70.0 7.00e-01 100.0% 83.2%
3738833 102.1.1.30 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HHH_8 0.85 58.0 6.78e-01 87.2% 100.0%
3704918 102.1.1.30 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HHH_8 0.83 66.0 6.80e-01 97.9% 86.7%
4927559 102.1.1.30 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HHH_8 0.77 69.0 7.12e-01 100.0% 98.9%
3512663 102.1.1.30 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HHH_8 0.68 61.0 6.23e-01 98.9% 100.0%
4034406 632.15.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › CompInhib_SCIN 0.64 41.0 4.26e-01 88.3% 70.6%
3722151 109.4.1.222 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DCB 0.62 52.0 4.04e-01 90.4% 43.6%
4657744 109.4.1.182 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec7-like_HUS,DCB 0.61 53.0 3.64e-01 92.6% 29.7%
3193435 3755.3.1.451 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › BUD22 0.61 51.0 4.59e-01 93.6% 74.1%
4305528 109.4.1.222 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DCB 0.61 50.0 3.77e-01 92.6% 37.7%
3192841 109.4.1.182 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec7-like_HUS,DCB 0.60 52.0 3.42e-01 92.6% 29.1%
3413715 109.4.1.182 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec7-like_HUS,DCB 0.60 50.0 3.15e-01 92.6% 17.8%
5013670 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.59 47.0 3.71e-01 84.0% 75.8%
3258508 109.4.1.182 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec7-like_HUS,DCB 0.59 52.0 3.51e-01 93.6% 36.1%
3640164 109.4.1.182 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec7-like_HUS,DCB 0.59 52.0 3.09e-01 95.7% 16.4%
4985470 4009.1.1.0 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.57 35.0 3.98e-01 81.9% 82.9%
3988314 1002.1.1.4 ↗ alpha complex topology › Fluoride ion channel › Fluoride ion channel › Fluoride ion channel › ThrE_2 0.57 47.0 4.20e-01 94.7% 61.8%
3963433 131.1.1.15 ↗ alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › Ppx-GppA_III 0.57 49.0 3.96e-01 100.0% 73.8%
4466618 1128.1.1.0 ↗ alpha bundles › LYR protein › LYR protein › LYR protein 0.56 36.0 3.79e-01 93.6% 72.9%
4016670 109.3.1.191 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › PF27566 0.55 42.0 3.04e-01 83.0% 43.3%
4940430 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.55 40.0 3.04e-01 77.7% 83.5%
5066642 4009.1.1.1 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › ARMT1-like_dom 0.54 33.0 3.72e-01 83.0% 81.4%
4032740 2484.1.1.102 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_ISL3 0.54 47.0 3.49e-01 96.8% 46.3%
4946843 4009.1.1.1 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › ARMT1-like_dom 0.53 36.0 4.16e-01 86.2% 100.0%
2774879 4244.1.1.2 ↗ a/b three-layered sandwiches › EreA/ChaN-like › EreA/ChaN-like › EreA/ChaN-like › Erythro_esteras 0.53 47.0 3.04e-01 96.8% 32.8%
3964011 633.21.1.1 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › DUF326 0.52 44.0 4.19e-01 90.4% 99.1%
4477947 2005.1.1.1 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1 0.52 45.0 3.15e-01 97.9% 40.0%
3413432 5048.1.1.0 ↗ alpha complex topology › Aquaporin-like › Aquaporin-like › Aquaporin-like 0.51 43.0 3.11e-01 92.6% 44.4%
3536812 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.51 41.0 3.64e-01 91.5% 100.0%
D3 medium residues 390-448
PDB
Domain cluster: rep: DNA_polymerase-beta_AP_pol__YP_008003963__Adoxophyes_honmai_entomopoxvirus_L__1293540__D394-443
D4 medium residues 454-540
PDB
Domain cluster: rep: LC554890.1__BCG50042.1__X__00024__D127-241
D5 medium residues 545-606
PDB
Domain cluster: rep: SR-VP_0-2_scaffold_141_316084_prodigal-single.1__X__X__00440__D267-324
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF14791.12 best DNA_pol_B_thumb 62.5 3.70e-17 95.2% 92.1%