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RNA-dependent_RNA_polymerase

Euk-Vir

Changjiang_astro-like_virus

RNA-dependent_RNA_polymerase__YP_009336808__Changjiang_astro-like_virus__1922764

Identity

Accession:
YP_009336808 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

81.3 mean pLDDT

Cluster

View cluster (450 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 355-436
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h5xA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.83 68.0 5.95e-01 100.0% 61.2%
1ra6A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.78 67.0 6.05e-01 100.0% 69.8%
5jxsA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.78 65.0 5.35e-01 100.0% 51.4%
6qwtA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.72 61.0 5.06e-01 100.0% 53.2%
2kt2A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 48.0 5.17e-01 96.3% 85.5%
1mukA02 3.90.1850.10 Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 0.68 62.0 3.75e-01 100.0% 17.5%
1yj7B01 3.30.70.1530 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Hypothetical protein rpa1041 0.65 41.0 4.37e-01 87.8% 73.2%
2cy8A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.61 44.0 3.34e-01 74.4% 55.5%
2if1A00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.60 43.0 3.75e-01 96.3% 49.2%
3l44A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.60 43.0 3.28e-01 74.4% 55.7%
6mfxA02 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.60 48.0 3.93e-01 89.0% 70.6%
3f0zA02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.59 43.0 3.89e-01 79.3% 100.0%
1vx7X00 3.30.1360.210 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.59 50.0 4.79e-01 100.0% 81.4%
3nx3A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.58 40.0 3.45e-01 100.0% 42.6%
2jhjA02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.57 44.0 3.96e-01 84.1% 98.3%
5t5sA01 3.10.310.40 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › 0.54 34.0 2.99e-01 91.5% 39.5%
1qd1A01 3.30.990.10 Alpha Beta › 2-Layer Sandwich › Formiminotransferase-cyclodeaminase; Chain B, domain 1 › Formiminotransferase, N-terminal subdomain 0.51 44.0 3.47e-01 100.0% 44.4%
3uuwB02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.51 40.0 3.17e-01 86.6% 75.0%
1w6kA01 6.20.120.20 Special › Other non-globular › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.50 28.0 3.25e-01 91.5% 84.0%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2541763 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.72 61.0 3.90e-01 100.0% 20.0%
3628456 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.71 33.0 2.80e-01 92.7% 29.7%
5063713 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.69 46.0 5.11e-01 95.1% 91.7%
4022087 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.69 62.0 5.07e-01 100.0% 68.7%
3602275 314.1.1.2 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.67 46.0 2.84e-01 70.7% 48.9%
5062182 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.66 41.0 4.45e-01 95.1% 78.5%
None — 0.66 52.0 3.50e-01 87.8% 66.0%
3301018 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.64 40.0 4.57e-01 89.0% 92.7%
5020779 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.62 40.0 4.44e-01 96.3% 88.3%
4970952 3715.1.1.1 ↗ a+b two layers › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal_L22e 0.61 46.0 4.58e-01 100.0% 78.8%
3927940 304.36.1.2 ↗ a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › RVT_1 0.60 50.0 4.64e-01 100.0% 72.4%
4018916 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.59 46.0 2.93e-01 87.8% 64.3%
4441063 102.1.2.1 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase › HhH-GPD 0.58 47.0 3.51e-01 90.2% 76.1%
5054374 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 26.0 3.14e-01 74.4% 64.8%
3909510 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 0.56 49.0 3.30e-01 100.0% 47.1%
5045662 102.1.2.1 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase › HhH-GPD 0.56 44.0 3.32e-01 87.8% 57.3%
5070153 5104.1.1.0 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases 0.54 31.0 2.81e-01 91.5% 36.5%
3892181 304.8.1.85 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › KH_PARP14_4 0.53 35.0 3.67e-01 87.8% 77.1%
5084053 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.53 46.0 3.39e-01 97.6% 63.0%
4182095 2004.1.1.80 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Cytidylate_kin 0.52 44.0 3.29e-01 97.6% 69.7%
3961149 7527.1.1.2 ↗ a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › CoA_transf_3 0.51 39.0 2.55e-01 93.9% 17.7%
D2 medium residues 42-84
PDB
D3 medium residues 85-114_263-277_437-525
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009330039__Hubei_sobemo-like_virus_44__1923232__D28-40_214-244_371-448
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4c1sA00 1.50.10.20 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.53 42.0 3.06e-01 85.1% 92.5%
4ctaA02 3.30.70.2860 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 26.0 3.29e-01 94.8% 81.3%
3renA00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.51 36.0 2.80e-01 74.6% 67.4%
3qxfA00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.51 38.0 2.87e-01 77.6% 89.6%
3kezA01 1.25.40.390 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.51 36.0 3.03e-01 73.1% 73.2%
2k19A00 1.20.1440.140 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.50 32.0 3.67e-01 91.8% 88.8%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1108483 109.2.1.13 ↗ alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid › Glyco_hydro_76 0.53 42.0 3.06e-01 85.1% 92.5%
3734599 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 43.0 3.57e-01 90.3% 69.6%
4449988 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 36.0 3.40e-01 72.4% 83.1%
D4 medium residues 115-160_194-216_235-262_293-352
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r7rA05 1.10.357.80 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.68 62.0 6.03e-01 100.0% 98.3%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2994348 304.48.1.9 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1,CoV_RPol_N 0.86 82.0 4.90e-01 100.0% 25.3%
217141 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 0.81 76.0 5.69e-01 100.0% 66.1%
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 0.80 75.0 5.43e-01 100.0% 61.1%
4875416 304.48.1.13 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flavi_NS5 0.77 73.0 5.31e-01 100.0% 58.7%
3960648 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 0.68 51.0 4.11e-01 78.3% 64.9%
D5 medium residues 161-193_217-234
PDB
Domain cluster: representative