←Back to structures

dna-pol

Euk-Vir

Catopsilia_pomona_nucleopolyhedrovirus

dna-pol__YP_009255332__Catopsilia_pomona_nucleopolyhedrovirus__1850906

Identity

Accession:
YP_009255332 ↗
Protein ID:
dna-pol
Kingdom:
euk

Quality

81.1 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Alphabaculovirus› Catopsilia_pomona_nucleopolyhedrovirus

TaxID: 1850906

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 medium residues 1-19_195-280
PDB
Domain cluster: rep: DNA_polymerase_elongation_subunit_family_B__YP_010088005__Lymphocystis_disease_virus_4__2704413__D159-241
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 32.0 1.20e-07 93.3% 38.0%
D2 medium residues 20-67_128-183_412-432
PDB
Domain cluster: rep: DNA_polymerase__YP_009666761__Mythimna_unipuncta_nucleopolyhedrovirus__447897__D1-67_114-188
D3 medium residues 68-127
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ezeB00 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.56 48.0 3.15e-01 100.0% 26.6%
1jyaB00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.54 42.0 3.40e-01 86.7% 53.7%
4xnhC00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 40.0 3.09e-01 88.3% 81.8%
4lbhA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.52 42.0 3.79e-01 98.3% 93.6%
6c80A03 3.40.462.10 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain 0.51 41.0 2.93e-01 98.3% 44.6%
3rtyB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.51 36.0 3.09e-01 78.3% 96.3%
5k8mA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 40.0 3.35e-01 98.3% 95.4%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3242923 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.54 37.0 2.93e-01 73.3% 75.4%
3997936 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.53 44.0 4.14e-01 95.0% 98.7%
D4 medium residues 184-194_281-349
PDB
Domain cluster: rep: DNA_polymerase__YP_008378438__Choristoneura_rosaceana_nucleopolyhedrovirus__58094__D271-327
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 24.4 2.50e-05 91.2% 28.9%
CATH (13)
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 0.80 70.0 5.06e-01 95.0% 74.6%
1q8iA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.79 68.0 5.10e-01 92.5% 73.0%
2v79A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.57 42.0 3.75e-01 77.5% 78.3%
6nvxB02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.55 38.0 3.94e-01 86.3% 76.6%
4xrtA02 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 38.0 3.13e-01 75.0% 85.6%
3n54B01 6.20.190.10 Special › Other non-globular › Nuclear Transport Factor 2; Chain: A, › Nutrient germinant receptor protein C, domain 1 0.53 29.0 3.30e-01 80.0% 70.5%
5ib9A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.53 42.0 2.91e-01 87.5% 80.7%
4mn5A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 37.0 3.49e-01 76.2% 69.9%
4wksC02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.52 36.0 3.74e-01 83.7% 77.3%
4yfbC02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.51 36.0 3.69e-01 85.0% 75.6%
1ry6A00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.51 39.0 2.71e-01 87.5% 79.9%
4r9iA01 3.30.497.10 Alpha Beta › 2-Layer Sandwich › Antithrombin; Chain I, domain 2 › Antithrombin, subunit I, domain 2 0.50 40.0 2.90e-01 92.5% 68.7%
1s67L00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.50 35.0 3.07e-01 72.5% 89.1%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4059788 387.1.1.24 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related › Toxin_35 0.64 36.0 3.94e-01 70.0% 67.7%
4617044 387.1.1.24 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related › Toxin_35 0.63 36.0 4.05e-01 70.0% 73.3%
3517917 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.54 35.0 3.73e-01 72.5% 78.5%
4639306 109.4.1.1255 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N, Cnd1 0.54 38.0 2.25e-01 75.0% 27.5%
4961794 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 38.0 3.25e-01 73.8% 60.0%
3486348 101.17.1.0 ↗ alpha arrays › HTH › IHF-like DNA-binding proteins › IHF-like DNA-binding proteins 0.53 32.0 3.52e-01 77.5% 73.8%
3788603 2004.1.1.250 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin,Microtub_bd 0.53 42.0 2.58e-01 93.8% 30.6%
3905156 4956.1.1.0 ↗ a+b two layers › ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.52 39.0 3.92e-01 80.0% 90.0%
3928418 3785.1.1.1 ↗ a+b three layers › Suppressor of Fused, C-terminal domain › Suppressor of Fused, C-terminal domain › Suppressor of Fused, C-terminal domain › SARA_C 0.51 41.0 3.43e-01 88.7% 95.7%
4934997 512.1.1.2 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_2nd 0.50 34.0 3.12e-01 72.5% 75.0%
4944869 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 41.0 3.50e-01 88.7% 77.7%
3230428 708.1.1.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.50 41.0 3.51e-01 90.0% 63.1%
D5 medium residues 350-411
PDB
Domain cluster: rep: DNA_polymerase_catalytic_subunit__YP_009342373__Spheniscid_alphaherpesvirus_1__2560777__D504-588
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4qclA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.89 83.0 5.23e-01 100.0% 24.0%
2gv9A03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.84 76.0 5.10e-01 100.0% 28.1%
1d5aA02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.81 73.0 4.95e-01 100.0% 29.0%
1noyB02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.79 69.0 4.61e-01 100.0% 26.1%
4fvmA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.79 70.0 4.66e-01 98.4% 27.4%
2e6mA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.75 70.0 4.82e-01 100.0% 34.4%
6y6hA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.59 46.0 3.40e-01 88.7% 51.7%
4gzcA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.56 41.0 3.27e-01 79.0% 77.3%
3cxbA01 3.30.2440.10 Alpha Beta › 2-Layer Sandwich › Secreted effector protein SifA fold › Secreted effector protein SifA 0.54 40.0 3.32e-01 83.9% 43.5%
3m7vA02 3.30.70.1250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Phosphopentomutase 0.54 41.0 3.34e-01 83.9% 67.8%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
None — 0.92 86.0 4.80e-01 100.0% 9.8%
None — 0.91 85.0 4.76e-01 100.0% 9.9%
3995965 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.91 85.0 5.84e-01 100.0% 36.8%
4972474 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.90 83.0 4.64e-01 100.0% 9.3%
5054032 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.90 83.0 4.97e-01 100.0% 17.8%
5081878 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.89 79.0 4.76e-01 100.0% 16.4%
5035328 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.89 82.0 5.36e-01 100.0% 28.5%
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 0.89 82.0 4.75e-01 100.0% 13.8%
3192875 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.89 82.0 4.72e-01 100.0% 13.9%
5025208 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.88 78.0 5.12e-01 100.0% 25.7%
5069333 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.88 78.0 4.65e-01 100.0% 15.7%
4874454 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.88 81.0 5.16e-01 100.0% 24.5%
4939488 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.87 78.0 4.88e-01 100.0% 20.7%
5067181 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.87 79.0 4.67e-01 100.0% 16.1%
5023018 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.86 74.0 4.98e-01 93.5% 28.6%
4981192 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.85 74.0 4.82e-01 100.0% 23.1%
5029084 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.85 77.0 5.13e-01 100.0% 29.3%
3794217 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.84 76.0 4.37e-01 100.0% 12.5%
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 0.84 75.0 4.24e-01 100.0% 9.8%
4997716 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 77.0 5.11e-01 100.0% 30.7%
5017082 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.84 73.0 4.47e-01 100.0% 16.9%
4958553 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 74.0 4.95e-01 100.0% 27.3%
2958185 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 75.0 4.79e-01 100.0% 23.1%
5068716 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.83 74.0 4.62e-01 100.0% 20.9%
4452101 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 74.0 4.98e-01 100.0% 29.5%
3520437 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 74.0 5.11e-01 100.0% 32.1%
4282509 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.81 73.0 4.20e-01 100.0% 11.0%
4951831 2484.1.1.68 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H_2 0.80 71.0 4.47e-01 100.0% 23.6%
4029124 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.79 68.0 4.44e-01 100.0% 22.7%
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 0.79 70.0 4.19e-01 100.0% 14.9%
4929239 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.59 48.0 3.18e-01 100.0% 20.0%
3927575 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.56 34.0 3.52e-01 88.7% 63.3%
3378866 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 33.0 3.35e-01 100.0% 68.3%
D6 medium residues 433-485_575-631
PDB
Domain cluster: rep: IMGVR_UViG_3300048031_000811-3300048031-Ga0494182_008429_2395_4416__D190-244_288-384
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 38.1 1.20e-09 90.0% 13.0%
D7 medium residues 486-526_541-574
PDB
Domain cluster: rep: DNA_polymerase__YP_009316112__Anticarsia_gemmatalis_multiple_nucleopolyhedrovirus__268591__D473-499_523-556
D8 medium residues 527-540_632-756
PDB
Domain cluster: rep: NC_004735.1__NP_835679.1__Rm378p092__00092__D1-33_185-289
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00136.27 best DNA_pol_B 58.0 1.10e-15 98.6% 26.9%
D9 medium residues 757-802_904-955_1009-1021
PDB
Domain cluster: rep: dna-pol__YP_009666600__Oxyplax_ochracea_nucleopolyhedrovirus__2083176__D730-794_872-935