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RNA_dependent_RNA_polymerase

Euk-Vir

Orsay_virus

RNA_dependent_RNA_polymerase__YP_009173859__Orsay_virus__977912

Identity

Accession:
YP_009173859 ↗
Protein ID:
RNA_dependent_RNA_polymerase
Kingdom:
euk

Quality

61.8 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Magsaviricetes› Nodamuvirales› Nodaviridae› Orsay_virus

TaxID: 977912

Cluster

Singleton — not in a non-trivial cluster

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 671-763
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2xgsB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.64 39.0 4.44e-01 83.9% 79.5%
1gvnA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.56 37.0 3.85e-01 100.0% 71.3%
4rg6A03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.56 39.0 3.44e-01 91.4% 50.4%
3ls1A00 1.20.120.290 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle 0.52 32.0 2.83e-01 93.5% 43.6%
D2 medium residues 123-232
PDB
D3 medium residues 413-460_532-565
PDB
Domain cluster: rep: hypothetical_protein_1__YP_009337425__Wenzhou_bivalvia_virus_3__1923555__D646-677_755-792
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2w00A02 3.90.640.50 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › 0.56 34.0 3.64e-01 82.9% 68.5%
1l1lA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.50 42.0 2.69e-01 100.0% 21.3%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3934288 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 0.75 65.0 4.98e-01 96.3% 87.4%
3708776 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 0.73 66.0 4.34e-01 100.0% 62.2%
3615476 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 0.72 65.0 4.31e-01 100.0% 63.4%
4262041 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 0.63 57.0 3.98e-01 100.0% 54.1%
4617426 513.1.1.1 ↗ a+b two layers › Obg GTP-binding protein C-terminal domain-like › Obg GTP-binding protein C-terminal domain › Obg GTP-binding protein C-terminal domain › DUF1967 0.59 51.0 4.96e-01 100.0% 87.8%
3935932 2006.1.1.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.53 44.0 3.25e-01 92.7% 73.5%
3997639 7563.1.1.0 ↗ a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related 0.52 43.0 2.93e-01 92.7% 67.0%
3998079 2003.1.2.9 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GDI 0.51 37.0 2.56e-01 78.0% 74.5%
3358438 109.4.1.363 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Tcf25 0.51 44.0 2.92e-01 100.0% 29.9%
D4 medium residues 461-531_566-670
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6qwtA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.75 58.0 6.45e-01 90.3% 99.3%
1jwwA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.71 34.0 4.89e-01 71.0% 100.0%
2r7rA04 3.30.70.2480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 49.0 5.20e-01 95.5% 84.1%
1earA02 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.63 26.0 3.90e-01 76.7% 92.8%
5mmjo00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.60 20.0 3.09e-01 75.6% 72.0%
3smzA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 36.0 4.34e-01 89.8% 94.6%
3mtkA00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.56 42.0 4.42e-01 82.4% 84.7%
3tvkA00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.54 43.0 4.43e-01 92.6% 85.5%
6hbzA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.54 41.0 4.36e-01 92.6% 88.1%
5t17A00 3.30.1340.10 Alpha Beta › 2-Layer Sandwich › Histidine-containing Protein; Chain: A; › HPr-like 0.52 20.0 2.75e-01 82.4% 65.9%
2f5gA00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.52 34.0 3.87e-01 74.4% 87.7%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4068028 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 0.69 58.0 4.86e-01 88.1% 62.4%
3737536 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 0.68 58.0 4.84e-01 89.2% 73.4%
3236725 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 0.67 59.0 5.12e-01 93.8% 77.7%
4981261 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.67 29.0 4.24e-01 76.1% 92.0%
5023633 304.24.1.5 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N 0.65 28.0 4.29e-01 77.3% 100.0%
3676014 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 0.64 58.0 3.97e-01 96.6% 39.5%
4934750 304.57.1.1 ↗ a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.63 36.0 4.49e-01 77.3% 90.9%
4524153 304.22.1.1 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C 0.57 26.0 3.57e-01 75.6% 85.9%
4995741 304.48.1.6 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_A 0.55 40.0 4.41e-01 74.4% 91.7%
4986600 304.8.1.12 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_8 0.55 32.0 3.79e-01 73.9% 84.2%
3677764 304.8.1.23 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N 0.54 41.0 4.55e-01 86.4% 99.3%
4115602 304.48.1.6 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_A 0.54 37.0 4.38e-01 71.6% 100.0%
3947798 304.8.1.70 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Phage_GPA 0.53 46.0 3.97e-01 93.8% 64.3%
4173640 304.55.1.27 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Phage_GPA 0.53 46.0 3.96e-01 93.8% 64.7%
4932798 304.8.1.81 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › REP_ORF2-G2P 0.51 39.0 3.93e-01 87.5% 80.0%