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RNA-dependent_RNA_polymerase

Euk-Vir

Beihai_weivirus-like_virus_4

RNA-dependent_RNA_polymerase__YP_009337162__Beihai_weivirus-like_virus_4__1922752

Identity

Accession:
YP_009337162 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

81.7 mean pLDDT

Cluster

View cluster (18 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 11-115
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337047__Beihai_weivirus-like_virus_7__1922754__D6-140
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.72 37.0 4.25e-01 83.8% 66.7%
2x3mA00 1.25.40.670 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.68 45.0 3.84e-01 82.9% 42.8%
2mabA00 1.10.10.1350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain 0.66 48.0 4.78e-01 92.4% 73.4%
2c42A03 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.66 43.0 3.46e-01 81.9% 33.0%
3fbzA01 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 48.0 4.93e-01 81.9% 80.4%
1oo0A00 3.30.1560.10 Alpha Beta › 2-Layer Sandwich › Mago nashi protein › Mago nashi 0.62 40.0 3.66e-01 100.0% 47.2%
1ldjA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.62 44.0 4.34e-01 85.7% 67.8%
2rn7A01 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 0.62 35.0 4.11e-01 88.6% 84.8%
3toyA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.61 40.0 3.82e-01 98.1% 55.1%
1bm9A00 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 0.58 35.0 3.34e-01 81.9% 51.7%
3msyA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.57 44.0 4.34e-01 81.9% 83.8%
5xdcB01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.55 36.0 3.59e-01 91.4% 63.1%
1e6bA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.54 32.0 3.15e-01 84.8% 53.2%
4jn7A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 40.0 3.89e-01 93.3% 69.7%
3m9vA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.53 38.0 3.55e-01 86.7% 61.4%
2whnA00 1.20.81.30 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › Type II secretion system (T2SS), domain F 0.52 39.0 3.91e-01 88.6% 75.5%
5gj7A01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.52 36.0 3.44e-01 84.8% 60.0%
3hvnA01 3.90.840.10 Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain 0.50 37.0 3.18e-01 78.1% 84.9%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4489939 101.35.1.4 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3 0.77 45.0 5.71e-01 88.6% 100.0%
3269592 198.1.1.2 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.73 45.0 4.88e-01 86.7% 75.3%
3248091 198.1.1.2 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.69 43.0 4.70e-01 85.7% 77.6%
3384318 601.33.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain 0.65 39.0 4.49e-01 78.1% 82.7%
3936293 198.1.1.3 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_1 0.65 40.0 4.23e-01 83.8% 68.4%
5001603 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.64 42.0 4.46e-01 81.9% 77.8%
3293481 861.1.1.1 ↗ a+b two layers › Mago nashi protein › Mago nashi protein › Mago nashi protein › Mago_nashi 0.63 39.0 3.72e-01 98.1% 51.2%
3470076 861.1.1.0 ↗ a+b two layers › Mago nashi protein › Mago nashi protein › Mago nashi protein 0.62 41.0 3.75e-01 100.0% 50.0%
3725909 284.1.3.1 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.61 36.0 3.78e-01 81.0% 63.8%
4090711 5067.1.1.8 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › HPP 0.60 47.0 4.08e-01 98.1% 54.4%
3244588 371.1.1.0 ↗ few secondary structure elements › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 0.58 45.0 4.79e-01 81.9% 97.8%
4112673 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.57 45.0 3.73e-01 82.9% 93.8%
3231297 189.1.1.2 ↗ alpha bundles › GTPase activation domain, GAP › GTPase activation domain, GAP › GTPase activation domain, GAP › RhoGAP 0.55 47.0 3.69e-01 92.4% 50.9%
3869172 5000.3.1.0 ↗ alpha arrays › Toxins' membrane translocation domains › Bcl-2 inhibitors of programmed cell death › Bcl-2 inhibitors of programmed cell death 0.53 47.0 4.13e-01 100.0% 76.2%
3266710 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.52 31.0 3.46e-01 87.6% 77.5%
3812869 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.52 37.0 3.81e-01 87.6% 79.0%
3253771 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.52 44.0 3.41e-01 92.4% 84.8%
3996406 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.51 29.0 3.40e-01 83.8% 81.4%
4959099 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.51 34.0 3.72e-01 96.2% 88.7%
4059028 109.21.1.3 ↗ alpha superhelices › Repetitive alpha hairpins › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Sec16_C 0.51 44.0 3.00e-01 94.3% 81.1%
3295575 284.1.3.2 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › OSR1_C 0.51 37.0 3.81e-01 91.4% 80.0%
5062669 632.23.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical linker domain in nicking endonuclease N.BspD6I › Helical linker domain in nicking endonuclease N.BspD6I 0.51 31.0 3.60e-01 81.0% 87.7%
3942280 2484.1.1.88 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ParM_N 0.51 36.0 3.08e-01 74.3% 71.2%
D2 medium residues 248-313
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7vjvA01 2.60.120.590 Mainly Beta › Sandwich › Jelly Rolls › Alpha-ketoglutarate-dependent dioxygenase AlkB-like 0.56 37.0 2.72e-01 71.2% 29.5%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5003452 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.59 36.0 2.94e-01 98.5% 30.8%
D3 medium residues 314-381_471-515
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.62 28.0 3.28e-01 92.0% 59.5%
4dylA02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.60 30.0 3.25e-01 96.5% 56.4%
3ma5A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 31.0 3.43e-01 75.2% 71.1%
2chpA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.53 29.0 2.66e-01 94.7% 37.8%
1w9cA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.53 41.0 2.98e-01 95.6% 29.3%
1oqcA00 1.20.120.310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain 0.51 36.0 3.68e-01 100.0% 73.2%
2va8A03 1.10.3380.30 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › 0.51 41.0 3.29e-01 85.0% 98.6%
1jr8A00 1.20.120.310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain 0.51 33.0 3.47e-01 94.7% 71.4%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3434397 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 43.0 3.43e-01 84.1% 86.0%
3886558 109.4.1.947 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_DAAF5 0.52 43.0 3.91e-01 90.3% 87.7%
3764822 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 34.0 3.23e-01 81.4% 57.5%
3710484 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.50 39.0 3.08e-01 85.8% 39.6%
D4 medium residues 382-445_459-470_516-552
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337141__Beihai_weivirus-like_virus_15__1922743__D392-442_461-485_531-592
D5 medium residues 446-458_553-628
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337183__Beihai_weivirus-like_virus_12__1922741__D575-645
D6 medium residues 629-797
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337047__Beihai_weivirus-like_virus_7__1922754__D604-746