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RNA-dependent_RNA_polymerase

Euk-Vir

Beihai_narna-like_virus_26

RNA-dependent_RNA_polymerase__YP_009333146__Beihai_narna-like_virus_26__1922454

Identity

Accession:
YP_009333146 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

75.0 mean pLDDT

Cluster

View cluster (39 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 1-104
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009329842__Hubei_narna-like_virus_24__1922955__D1-131
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.65 39.0 4.60e-01 77.9% 85.1%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.62 37.0 4.21e-01 77.9% 81.3%
3vbbE01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.61 38.0 3.62e-01 70.2% 54.6%
3ha4B00 1.20.58.690 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 39.0 3.76e-01 80.8% 56.7%
1jqjC02 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.57 44.0 4.57e-01 82.7% 89.6%
2wdoA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.57 34.0 3.29e-01 99.0% 49.6%
1nxuA01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.57 39.0 4.40e-01 98.1% 92.4%
1c9bA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.55 40.0 4.12e-01 96.2% 80.4%
3ciaA03 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.54 42.0 3.67e-01 81.7% 93.5%
1m2vB01 1.20.120.730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sec23/Sec24 helical domain 0.54 45.0 3.80e-01 89.4% 58.0%
4nxtA01 1.10.1410.40 Mainly Alpha › Orthogonal Bundle › Poly(a)-polymerase, middle domain › 0.51 43.0 3.92e-01 97.1% 66.9%
2xq0A03 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.51 40.0 3.53e-01 84.6% 93.6%
2uyyA02 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 0.50 34.0 3.29e-01 70.2% 61.0%
8e83B01 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.50 44.0 2.97e-01 100.0% 70.0%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3634447 4207.1.2.0 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region 0.65 42.0 4.21e-01 93.3% 64.8%
3896924 320.4.1.5 ↗ a+b two layers › R3H domain-like › PUB domain › PUB domain › Gasdermin_C 0.64 53.0 4.29e-01 92.3% 45.9%
5056442 601.18.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 0.62 41.0 3.96e-01 81.7% 60.0%
4051269 610.2.1.1 ↗ alpha arrays › ERP29 C domain-like › Helical domain of Sec23/24 › Helical domain of Sec23/24 › Sec23_helical 0.60 44.0 4.39e-01 87.5% 73.6%
3451722 3930.1.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.59 53.0 5.04e-01 100.0% 92.8%
4075943 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.58 48.0 4.62e-01 90.4% 79.2%
3652633 3930.1.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.58 53.0 4.95e-01 100.0% 82.3%
5076914 563.2.1.0 ↗ alpha bundles › ATPD N-terminal domain-like › Cas Cmr5-like › Cas Cmr5-like 0.58 47.0 4.55e-01 90.4% 100.0%
3969307 138.1.1.6 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA_pol3_delt_C 0.57 44.0 4.13e-01 83.7% 80.0%
3799135 633.15.1.0 ↗ alpha bundles › Bromodomain-like › alpha-ketoacid dehydrogenase kinase-N › alpha-ketoacid dehydrogenase kinase-N 0.56 50.0 4.46e-01 100.0% 72.7%
3592428 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.55 38.0 3.37e-01 70.2% 68.3%
1487362 3930.2.1.1 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in endoribonuclease Dicer › Helical bundle in endoribonuclease Dicer › Dicer_PBD 0.54 44.0 4.27e-01 100.0% 79.0%
3337031 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.54 44.0 3.62e-01 86.5% 64.4%
4979232 3930.1.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.52 47.0 4.35e-01 100.0% 93.3%
D2 medium residues 105-147_243-381
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF05919.17 best Mitovir_RNA_pol 65.9 5.20e-18 79.1% 23.9%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mukA02 3.90.1850.10 Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 0.77 71.0 5.04e-01 98.9% 67.3%
3e9lA02 1.20.80.40 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › Prp8 RNase H domain, fingers region 0.56 25.0 3.43e-01 96.2% 80.0%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3789227 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.81 70.0 5.74e-01 90.1% 85.5%
3772920 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.80 75.0 6.23e-01 98.9% 98.0%
1697857 304.48.1.30 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › CPV_RdRP_pol_dom 0.78 72.0 5.77e-01 98.9% 86.4%
4019374 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 0.77 72.0 5.45e-01 100.0% 80.5%
3691350 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.77 71.0 6.13e-01 97.8% 99.3%
3336938 304.48.1.43 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mitovir_RNA_pol 0.75 69.0 6.07e-01 96.2% 70.4%
3907339 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 0.60 43.0 3.88e-01 100.0% 54.3%
3185865 2004.1.1.184 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.52 41.0 3.20e-01 83.0% 81.0%
D3 medium residues 148-242
PDB
Domain cluster: representative
D4 medium residues 615-672
PDB