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RNA_replicase_component

Euk-Vir

Ribgrass_mosaic_virus

RNA_replicase_component__YP_005476601__Ribgrass_mosaic_virus__51680

Identity

Accession:
YP_005476601 ↗
Protein ID:
RNA_replicase_component
Kingdom:
euk

Quality

75.6 mean pLDDT

Cluster

View cluster (21 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 368-502
PDB
D2 high residues 697-809
PDB
Domain cluster: rep: replicase__NP_059451__Soil-borne_cereal_mosaic_virus__100887__D845-991
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF20896.3 best ToMV_Hel_N 60.0 4.30e-16 83.2% 62.7%
D3 high residues 821-954
PDB
Domain cluster: rep: KX578043.1__AOT27930.1__X__00015__D87-267
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01443.25 best Viral_helicase1 100.4 1.90e-28 97.8% 50.4%
D4 medium residues 18-79
PDB
Domain cluster: rep: unnamed_protein_product__NP_046152__Turnip_vein-clearing_virus__29272__D29-80
D5 medium residues 99-209
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01660.23 best Vmethyltransf 62.9 3.80e-17 100.0% 28.0%
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2nxcA03 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.66 48.0 4.28e-01 100.0% 54.2%
5cm2Z00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.65 48.0 4.04e-01 100.0% 46.2%
1zcjA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.65 55.0 4.64e-01 99.1% 54.9%
3merA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.65 47.0 4.08e-01 100.0% 48.6%
3mggB01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.64 49.0 4.31e-01 100.0% 54.9%
3eagA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.63 44.0 4.80e-01 97.3% 87.1%
4bujE03 1.10.3380.30 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › 0.60 50.0 3.94e-01 88.3% 57.8%
4om8A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 48.0 4.14e-01 99.1% 54.1%
1f14A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 52.0 4.36e-01 100.0% 56.1%
4inoA01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.59 43.0 4.06e-01 100.0% 63.2%
3g0oA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 38.0 3.38e-01 97.3% 47.0%
1dl5A01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.56 48.0 3.94e-01 100.0% 52.2%
3q2iA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 38.0 3.44e-01 99.1% 50.6%
3jruA01 3.40.220.10 Alpha Beta › 3-Layer(aba) Sandwich › Leucine Aminopeptidase, subunit E; domain 1 › Leucine Aminopeptidase, subunit E, domain 1 0.54 39.0 3.48e-01 75.7% 61.3%
2egvA02 3.40.1280.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha/beta knot › SPOUT methyltransferase, trefoil knot domain 0.54 46.0 4.16e-01 98.2% 77.9%
3d40A00 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.54 47.0 3.71e-01 100.0% 79.4%
4dcmA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 48.0 4.15e-01 100.0% 66.7%
4kp1A02 3.30.499.10 Alpha Beta › 2-Layer Sandwich › Aconitase; domain 3 › Aconitase, domain 3 0.52 43.0 3.97e-01 98.2% 68.2%
2d4aD01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 42.0 3.94e-01 95.5% 70.2%
3bulA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.52 37.0 4.10e-01 75.7% 97.7%
2ongA01 1.50.10.130 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Terpene synthase, N-terminal domain 0.51 43.0 3.54e-01 91.9% 93.1%
1lvlA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 45.0 3.62e-01 96.4% 70.5%
1v6zA02 3.40.1280.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha/beta knot › SPOUT methyltransferase, trefoil knot domain 0.51 44.0 3.95e-01 97.3% 72.8%
5bu9A00 3.20.20.300 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycoside hydrolase, family 3, N-terminal domain 0.51 42.0 3.05e-01 91.9% 87.0%
1auaA01 3.40.525.10 Alpha Beta › 3-Layer(aba) Sandwich › Phosphatidylinositol Transfer Protein Sec14p › CRAL-TRIO lipid binding domain 0.50 42.0 3.45e-01 92.8% 78.4%
1vhkA02 3.40.1280.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha/beta knot › SPOUT methyltransferase, trefoil knot domain 0.50 43.0 3.89e-01 98.2% 75.3%
3e1tA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.50 42.0 3.29e-01 96.4% 41.4%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4002718 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.70 53.0 4.27e-01 100.0% 42.4%
5030542 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.68 51.0 4.73e-01 100.0% 62.9%
5000126 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.67 49.0 4.36e-01 100.0% 54.2%
4021707 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.61 54.0 4.18e-01 100.0% 43.5%
3472180 109.4.1.32 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G 0.61 47.0 3.55e-01 82.9% 80.4%
3694302 7512.1.1.54 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Alg14 0.59 52.0 4.03e-01 100.0% 63.1%
4196469 2003.1.5.23 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_4 0.59 43.0 3.67e-01 96.4% 46.5%
3689294 2003.1.1.69 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short_C2 0.58 50.0 3.80e-01 98.2% 51.4%
5017458 2003.1.1.311 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Fibrillarin_2 0.57 41.0 4.31e-01 100.0% 84.0%
4002736 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.56 48.0 4.12e-01 100.0% 57.3%
3723254 2003.1.1.69 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short_C2 0.56 49.0 3.76e-01 100.0% 47.0%
3707968 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.53 40.0 3.98e-01 79.3% 86.1%
3665653 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.53 42.0 3.92e-01 84.7% 87.1%
4990014 7512.1.1.3 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 0.53 46.0 3.83e-01 96.4% 85.5%
3435216 2005.1.1.41 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.53 46.0 4.04e-01 100.0% 69.7%
4933886 7512.1.1.3 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 0.52 46.0 3.90e-01 97.3% 85.9%
3729027 2003.1.1.20 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase 0.52 46.0 3.33e-01 98.2% 40.0%
3937962 2007.9.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Toll/Interleukin receptor TIR domain › Toll/Interleukin receptor TIR domain 0.51 41.0 3.64e-01 86.5% 67.5%
3720945 2003.1.1.3 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.51 44.0 3.39e-01 97.3% 49.2%
3987357 7516.1.1.1 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › NTP_transferase 0.51 43.0 3.33e-01 96.4% 80.0%
4369287 2002.1.1.69 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › MM_CoA_mutase 0.50 45.0 2.91e-01 100.0% 49.8%
4378767 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.50 43.0 3.40e-01 97.3% 48.6%
D6 medium residues 551-614
PDB
D7 medium residues 962-1099
PDB
Domain cluster: rep: TGB1_protein__NP_619560__Garlic_latent_virus__12458__D129-228
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01443.25 best Viral_helicase1 66.7 3.80e-18 83.3% 41.2%