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RNA-dependent_RNA_polymerase

Euk-Vir

Beihai_noda-like_virus_11

RNA-dependent_RNA_polymerase__YP_009333380__Beihai_noda-like_virus_11__1922464

Identity

Accession:
YP_009333380 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

78.7 mean pLDDT

Cluster

View cluster (17 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 18-82
PDB
D2 high residues 91-248_289-311
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337879__Hubei_noda-like_virus_9__1922989__D136-259_287-345
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19222.6 best Noda_Vmethyltr 201.7 6.60e-60 81.2% 97.3%
D3 high residues 782-922
PDB
Domain cluster: rep: hypothetical_protein__YP_009337806__Shuangao_insect_virus_11__1923467__D743-868
D4 medium residues 334-426
PDB
Domain cluster: rep: hypothetical_protein__YP_009336769__Hubei_diptera_virus_16__1922877__D264-353
D5 medium residues 600-632_697-781
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181
D6 medium residues 633-696
PDB
Domain cluster: rep: protein_A__NP_689439__Boolarra_virus__12286__D596-650
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2vx2G02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.73 45.0 4.78e-01 79.7% 72.7%
2a72A00 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.68 44.0 3.50e-01 81.2% 32.3%
3nynA03 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.67 44.0 4.13e-01 82.8% 54.3%
3c4wB01 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.63 42.0 3.01e-01 82.8% 22.3%
4akrA01 3.30.1140.60 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › F-actin capping protein, alpha subunit 0.63 38.0 3.30e-01 79.7% 36.8%
3lapA01 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 34.0 3.40e-01 92.2% 48.5%
6hj2A00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.61 42.0 2.80e-01 71.9% 23.7%
1fthA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.60 47.0 3.96e-01 89.1% 54.7%
2r0rB00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.59 39.0 3.74e-01 98.4% 56.4%
8jx6A02 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.57 36.0 3.14e-01 79.7% 38.8%
4ha8A01 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 32.0 3.30e-01 71.9% 54.0%
2z3gB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.57 42.0 3.37e-01 79.7% 79.5%
5b3hC01 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.56 27.0 3.07e-01 70.3% 56.2%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.55 38.0 3.99e-01 75.0% 79.7%
4fqdB02 3.65.10.10 Alpha Beta › Alpha-beta prism › UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain › Enolpyruvate transferase domain 0.54 34.0 2.38e-01 82.8% 19.0%
6ketA01 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.53 39.0 2.52e-01 79.7% 34.2%
1bbyA00 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 0.53 32.0 3.19e-01 79.7% 55.1%
3p26A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 43.0 2.98e-01 90.6% 27.9%
3dlcA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 43.0 3.14e-01 100.0% 87.2%
4tv7D01 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 0.52 36.0 3.34e-01 81.2% 55.3%
6gyhA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.52 43.0 3.10e-01 100.0% 45.8%
4qmfB01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.51 42.0 3.93e-01 95.3% 81.7%
6njeA00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.50 41.0 2.76e-01 96.9% 65.0%
1ewqA04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.50 36.0 2.94e-01 79.7% 69.9%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5366 304.48.1.15 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3 0.90 82.0 4.90e-01 100.0% 15.8%
5026627 4961.1.1.0 ↗ a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit 0.64 44.0 3.79e-01 79.7% 46.0%
3716558 70.3.1.1 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like › SET 0.63 47.0 3.19e-01 81.2% 50.4%
3261151 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.61 41.0 2.71e-01 82.8% 15.3%
4106869 101.1.2.20 ↗ alpha arrays › HTH › HTH › winged helix domain › Arg_repressor 0.61 36.0 3.54e-01 96.9% 51.4%
3942719 4053.1.1.0 ↗ a+b complex topology › Insertion domain in replication terminator protein (Tus) › Insertion domain in replication terminator protein (Tus) › Insertion domain in replication terminator protein (Tus) 0.60 40.0 4.21e-01 92.2% 81.8%
3735563 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.59 45.0 3.51e-01 84.4% 91.3%
3674655 2003.1.9.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins 0.59 49.0 2.92e-01 100.0% 11.6%
4645593 140.1.1.0 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.58 35.0 2.80e-01 81.2% 27.5%
3210565 101.1.2.267 ↗ alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.56 44.0 3.41e-01 85.9% 87.6%
5016111 192.11.1.0 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB 0.55 34.0 3.60e-01 79.7% 70.9%
4646512 633.6.1.3 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › HpaB 0.54 46.0 3.28e-01 100.0% 63.6%
4043003 601.7.1.6 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › GlnD_UR_UTase 0.54 38.0 2.89e-01 76.6% 31.2%
3405298 70.3.1.0 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like 0.54 39.0 2.66e-01 79.7% 81.1%
5073006 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.54 39.0 2.97e-01 79.7% 77.5%
3609775 109.20.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Coatomer subunit alpha C-terminal domain › Coatomer subunit alpha C-terminal domain › COPI_C 0.53 43.0 3.00e-01 95.3% 51.8%
4002132 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.53 44.0 2.89e-01 98.4% 89.8%
3949634 148.1.3.23 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_6 0.53 43.0 3.69e-01 96.9% 56.5%
3432388 109.4.1.43 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SAC3_GANP 0.53 32.0 2.51e-01 71.9% 26.0%
3399732 3016.1.1.22 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › PDXDC1-like_cen2 0.53 40.0 3.52e-01 87.5% 96.2%
None — 0.52 44.0 2.86e-01 100.0% 87.5%
3711640 2006.1.1.4 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › NIF 0.51 42.0 3.11e-01 96.9% 89.5%
3924514 109.4.1.83 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Suf 0.51 42.0 2.73e-01 92.2% 75.9%
4019876 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 42.0 3.67e-01 93.8% 94.0%
5040756 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.51 39.0 3.47e-01 84.4% 85.3%
3201844 101.1.2.45 ↗ alpha arrays › HTH › HTH › winged helix domain › SAC3_GANP 0.51 37.0 3.25e-01 81.2% 92.4%
3364438 101.1.2.75 ↗ alpha arrays › HTH › HTH › winged helix domain › TFIIF_alpha 0.51 38.0 3.78e-01 85.9% 80.0%
3721713 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 37.0 3.68e-01 85.9% 74.3%
3956498 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.50 42.0 2.77e-01 100.0% 37.5%