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RNA_dependent_RNA_polymerase

Euk-Vir

Yado-nushi_virus_1-A

RNA_dependent_RNA_polymerase__YP_009551446__Yado-nushi_virus_1-A__2094187

Identity

Accession:
YP_009551446 ↗
Protein ID:
RNA_dependent_RNA_polymerase
Kingdom:
euk

Quality

39.5 mean pLDDT

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 141-285
PDB
Domain cluster: rep: VP2__YP_009665170__Eriocheir_sinensis_reovirus__273810__D721-872
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2bbwA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.73 66.0 5.76e-01 100.0% 94.5%
1knqA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.72 66.0 6.27e-01 100.0% 95.9%
3lv8A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.71 64.0 5.71e-01 100.0% 95.6%
1bifA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.70 64.0 5.68e-01 100.0% 98.5%
1e9fA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.70 63.0 5.69e-01 100.0% 91.1%
2f6rA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.70 63.0 5.41e-01 100.0% 88.3%
2plrA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.69 62.0 5.52e-01 100.0% 95.8%
2grjA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.69 62.0 5.82e-01 100.0% 98.3%
2jaqA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 62.0 5.70e-01 100.0% 98.9%
1rkbA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 62.0 5.86e-01 100.0% 91.3%
4gp6A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 63.0 5.94e-01 100.0% 94.2%
2bwjA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 61.0 5.55e-01 100.0% 94.4%
3nwjA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.67 60.0 5.50e-01 100.0% 89.7%
2pt5B00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.66 60.0 5.71e-01 99.3% 96.4%
1jjvA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.66 59.0 5.38e-01 100.0% 93.8%
4cvnA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.64 58.0 5.41e-01 100.0% 85.5%
4loaA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.64 58.0 5.64e-01 100.0% 98.1%
3kfvA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.64 57.0 5.81e-01 99.3% 99.3%
6hqvA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 55.0 5.26e-01 97.9% 98.8%
1dekA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 46.0 5.07e-01 97.2% 100.0%
4zo4A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 53.0 4.80e-01 100.0% 96.0%
3gemD00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 53.0 4.62e-01 100.0% 91.1%
4wsiB03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 53.0 4.71e-01 100.0% 89.6%
8hi4A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 47.0 3.95e-01 91.0% 99.6%
3gffA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 50.0 3.94e-01 99.3% 70.6%
1ihuA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 48.0 3.92e-01 97.2% 96.2%
5t5qB00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 49.0 4.25e-01 99.3% 90.6%
2i6qA01 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.55 50.0 4.35e-01 100.0% 96.8%
4ja0D02 3.40.50.1970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 44.0 4.65e-01 99.3% 97.7%
4yacA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 48.0 4.21e-01 97.9% 93.9%
3hcwA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 43.0 4.44e-01 100.0% 90.0%
1aukA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.53 48.0 3.57e-01 100.0% 85.2%
5if3B00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 44.0 3.95e-01 92.4% 85.6%
7fevA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 45.0 3.32e-01 95.2% 81.4%
3nv7A00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.52 31.0 3.07e-01 100.0% 53.5%
7e6iA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 43.0 4.08e-01 90.3% 100.0%
2ha9B00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.50 40.0 2.89e-01 83.4% 86.3%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4389171 2004.1.1.41 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ADK 0.73 67.0 6.26e-01 98.6% 97.7%
None — 0.73 67.0 6.15e-01 100.0% 91.0%
4587249 2004.1.1.79 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Thymidylate_kin 0.72 66.0 6.01e-01 100.0% 98.9%
4436757 2004.1.1.41 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ADK 0.71 65.0 5.73e-01 100.0% 99.5%
4134494 2004.1.1.192 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_18 0.70 64.0 5.88e-01 100.0% 82.5%
3860398 2004.1.1.41 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ADK 0.69 63.0 5.34e-01 100.0% 90.8%
4127347 2004.1.1.60 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SKI 0.69 63.0 6.11e-01 100.0% 100.0%
4935646 2004.1.1.192 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_18 0.68 61.0 5.65e-01 100.0% 96.3%
3406795 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.68 61.0 5.43e-01 100.0% 93.8%
4946615 2004.1.1.192 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_18 0.68 61.0 5.89e-01 100.0% 98.2%
5080212 2004.1.1.188 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Cytidylate_kin2 0.67 60.0 5.48e-01 100.0% 88.7%
5000470 2004.1.1.188 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Cytidylate_kin2 0.66 60.0 5.50e-01 100.0% 92.6%
5022283 2004.1.1.163 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › KTI12 0.65 59.0 5.57e-01 100.0% 94.9%
3719505 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.65 58.0 4.96e-01 100.0% 98.8%
3588578 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.64 58.0 5.46e-01 100.0% 100.0%
4284801 2003.1.6.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like › Tubulin 0.62 57.0 4.78e-01 100.0% 84.9%
3492560 2003.1.6.6 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like › Misat_Tub_SegII+Tubulin_3 0.62 56.0 4.59e-01 100.0% 96.4%
3524949 2004.1.1.50 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Guanylate_kin 0.62 56.0 5.21e-01 100.0% 92.4%
4013543 2003.1.6.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like 0.60 54.0 4.39e-01 100.0% 98.9%
5001336 2002.1.1.83 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_1 0.58 46.0 3.41e-01 85.5% 73.4%
3473091 2003.1.6.3 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like › Tubulin_3 0.56 39.0 3.86e-01 70.3% 94.2%
3291452 7579.1.1.6 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.55 48.0 4.13e-01 100.0% 88.9%
3943165 2007.1.2.2 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › Peripla_BP_1 0.54 41.0 4.27e-01 100.0% 87.4%
4853371 2005.1.1.24 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › DPRP 0.53 34.0 3.80e-01 98.6% 82.3%
5080445 2006.1.1.18 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › HAD_2 0.53 47.0 4.01e-01 98.6% 95.0%
3624403 7570.1.1.4 ↗ a/b three-layered sandwiches › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › PF27239 0.53 43.0 4.18e-01 89.0% 86.1%
3568403 2007.5.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › SASA 0.53 47.0 3.79e-01 98.6% 97.5%
4933177 2007.22.1.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Methyl-viologen reducing hydrogenase subunit D › Methyl-viologen reducing hydrogenase subunit D › FlpD 0.53 41.0 4.00e-01 100.0% 74.4%
4975451 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 47.0 3.98e-01 100.0% 90.8%
4934100 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 38.0 3.98e-01 91.7% 83.1%
3593952 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 46.0 4.09e-01 100.0% 93.0%
4996689 2004.1.1.16 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Arf 0.51 46.0 3.99e-01 100.0% 97.9%
5049732 7529.1.1.1 ↗ a/b three-layered sandwiches › Macro domain-like › Macro domain-like › Macro domain-like › Macro 0.51 41.0 3.90e-01 86.2% 99.4%
5039355 2006.1.6.15 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › DUF58 0.51 45.0 3.93e-01 97.9% 96.0%
3618569 2007.5.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase 0.51 44.0 3.73e-01 97.9% 98.1%
4865145 2006.1.6.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.51 43.0 3.90e-01 92.4% 95.5%
3811555 2003.1.5.31 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GRAS 0.50 43.0 3.22e-01 95.2% 77.7%
4955582 2007.22.1.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Methyl-viologen reducing hydrogenase subunit D › Methyl-viologen reducing hydrogenase subunit D › FlpD 0.50 40.0 3.94e-01 100.0% 79.4%
2100251 2003.1.1.3 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.50 42.0 3.90e-01 91.0% 95.7%
D2 high residues 377-465
PDB
D3 medium residues 45-94
PDB
D4 medium residues 115-140_290-370
PDB
D5 medium residues 535-598
PDB
D6 medium residues 750-870
PDB