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RNA-dependent_RNA_polymerase

Euk-Vir

Changjiang_narna-like_virus_3

RNA-dependent_RNA_polymerase__YP_009337343__Changjiang_narna-like_virus_3__1922778

Identity

Accession:
YP_009337343 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

80.5 mean pLDDT

Cluster

View cluster (2 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 medium residues 42-162
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009336702__Sanxia_narna-like_virus_1__1923360__D52-159
D2 medium residues 183-219_381-442
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4n7bA01 3.40.1010.20 Alpha Beta › 3-Layer(aba) Sandwich › Cobalt-precorrin-4 Transmethylase; domain 1 › 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain 0.55 31.0 2.99e-01 92.9% 46.6%
7x0fB01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.52 26.0 3.05e-01 74.7% 67.1%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5049970 181.1.1.0 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins 0.52 39.0 3.19e-01 77.8% 75.0%
3971485 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.51 44.0 3.56e-01 93.9% 68.1%
D3 medium residues 317-380_443-535
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337087__Hubei_narna-like_virus_4__1922958__D375-415_481-588
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gx5A03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.81 56.0 6.35e-01 70.1% 100.0%
4hkqA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.77 59.0 6.19e-01 91.1% 86.8%
7uinD01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.76 61.0 5.95e-01 82.8% 100.0%
4ol8A01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.75 53.0 5.72e-01 88.5% 83.7%
1s48A04 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.66 46.0 5.39e-01 72.0% 100.0%
3mahA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.64 30.0 4.32e-01 75.8% 98.6%
7e6gA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.64 48.0 4.93e-01 77.1% 87.2%
2dt9A01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.62 30.0 4.37e-01 75.2% 100.0%
3hvwA00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.61 48.0 4.81e-01 80.9% 82.4%
6eibD00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.61 47.0 4.80e-01 80.3% 85.3%
6zxbA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.61 46.0 4.80e-01 77.7% 92.4%
4zmuA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.61 48.0 4.92e-01 83.4% 87.1%
4er8A00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.58 40.0 4.02e-01 70.7% 94.5%
2cdqA03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.58 31.0 4.16e-01 75.8% 98.8%
2j0wA03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.57 30.0 4.08e-01 75.8% 98.8%
4x0qA03 3.30.70.370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 44.0 4.57e-01 80.9% 92.3%
1ewqA04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.54 27.0 2.92e-01 81.5% 52.2%
4lowA00 3.30.1360.20 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Transcriptional coactivator/pterin dehydratase 0.54 30.0 3.85e-01 76.4% 100.0%
3kizA02 3.90.650.10 Alpha Beta › Alpha-Beta Complex › Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 › PurM-like C-terminal domain 0.53 42.0 3.72e-01 82.8% 97.8%
3viuA04 3.90.650.10 Alpha Beta › Alpha-Beta Complex › Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 › PurM-like C-terminal domain 0.53 40.0 3.89e-01 78.3% 94.2%
1gpjA01 3.30.460.30 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Glutamyl-tRNA reductase, N-terminal domain 0.52 37.0 3.83e-01 71.3% 99.3%
4ammA00 3.40.366.10 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 0.52 40.0 2.98e-01 79.0% 48.2%
6fijA02 3.40.366.10 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 0.50 38.0 2.98e-01 78.3% 66.7%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3483524 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 0.77 68.0 5.41e-01 94.3% 69.8%
3934202 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 0.74 54.0 5.59e-01 73.9% 100.0%
3938275 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 0.70 64.0 5.32e-01 96.8% 63.1%
3209439 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 0.69 54.0 4.25e-01 82.8% 98.1%
3518893 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 56.0 4.83e-01 87.3% 60.8%
3939178 304.48.1.37 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_2 0.68 61.0 5.74e-01 96.8% 97.8%
3932482 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 62.0 5.24e-01 97.5% 66.1%
4115819 304.48.1.48 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GGDEF_2 0.64 46.0 4.55e-01 75.2% 85.3%
3926952 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 55.0 4.66e-01 95.5% 57.6%
5083386 304.12.1.0 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 0.61 37.0 4.66e-01 74.5% 100.0%
3356626 304.48.1.21 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Thg1,Thg1C 0.57 40.0 4.01e-01 71.3% 81.2%
3615047 304.112.1.0 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.57 33.0 4.20e-01 70.1% 100.0%
4934080 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.56 39.0 4.03e-01 70.7% 88.0%
5031817 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.55 39.0 4.04e-01 70.7% 91.0%
4999243 304.111.1.1 ↗ a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.55 39.0 3.73e-01 72.0% 99.4%
5056779 304.111.1.1 ↗ a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.55 41.0 4.23e-01 76.4% 97.9%
4947692 304.1.1.0 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain 0.53 34.0 3.94e-01 84.1% 89.6%
4257652 304.111.1.1 ↗ a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.52 40.0 3.89e-01 78.3% 95.9%
5048034 304.111.1.1 ↗ a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.52 39.0 3.87e-01 78.3% 97.6%
5051326 304.111.1.1 ↗ a+b two layers › Alpha-beta plaits › PurM C-terminal domain-like › PurM C-terminal domain-like › AIRS_C 0.52 39.0 3.73e-01 78.3% 93.4%
5053873 5104.1.1.1 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.51 28.0 3.33e-01 71.3% 78.1%
4989701 304.1.1.0 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain 0.50 34.0 3.78e-01 99.4% 89.2%
D4 medium residues 536-615
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5tgtA02 1.10.10.350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.62 45.0 3.93e-01 76.2% 56.1%
2b8iA00 1.20.1280.100 Mainly Alpha › Up-down Bundle › Monooxygenase › Pas factor, saposin domain 0.62 42.0 4.30e-01 88.7% 72.7%
2p11A02 1.10.286.50 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.61 38.0 3.93e-01 76.2% 66.2%
3vfcA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.57 42.0 3.47e-01 78.8% 50.3%
1su0B00 3.90.1010.10 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.57 47.0 3.99e-01 92.5% 97.8%
3qwwA03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.55 44.0 3.42e-01 90.0% 60.2%
1txuA01 1.10.246.120 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.55 45.0 4.28e-01 90.0% 81.9%
4akrA01 3.30.1140.60 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › F-actin capping protein, alpha subunit 0.55 46.0 4.19e-01 92.5% 85.8%
2wghA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.55 43.0 2.60e-01 88.7% 76.4%
4g3hC00 3.40.800.10 Alpha Beta › 3-Layer(aba) Sandwich › Arginase; Chain A › Ureohydrolase domain 0.54 43.0 2.96e-01 90.0% 53.2%
2ptfB02 1.20.58.290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. 0.53 36.0 4.08e-01 76.2% 100.0%
2wzkA01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.52 42.0 3.75e-01 93.8% 88.2%
3vwaA03 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.52 46.0 3.14e-01 100.0% 29.5%
1hh8A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 41.0 3.22e-01 90.0% 43.8%
4hz4A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 38.0 3.52e-01 81.2% 85.7%
3ieeA02 1.20.58.820 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Uncharacterised protein PF12889, C-terminal DUF3829 0.52 37.0 3.48e-01 77.5% 78.6%
4c9bB00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.51 41.0 2.88e-01 91.3% 29.6%
1r8gA00 3.30.590.20 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › 0.51 45.0 2.96e-01 100.0% 82.7%
2acxA01 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.50 37.0 2.87e-01 81.2% 39.0%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4011283 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.66 41.0 3.72e-01 73.8% 45.5%
3179519 101.1.2.381 ↗ alpha arrays › HTH › HTH › winged helix domain › UBR1-like_wing 0.61 43.0 3.62e-01 81.2% 43.7%
4437441 109.4.1.1333 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Vps35, PF27614 0.57 49.0 3.37e-01 100.0% 39.0%
4966102 223.1.1.3 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.56 43.0 3.37e-01 85.0% 93.5%
4950306 109.4.1.3617 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF7017 0.54 46.0 3.27e-01 100.0% 29.5%
4027274 273.1.1.2 ↗ a+b three layers › PR-1-like › PR-1-like › PR-1-like › CEP76_C 0.52 38.0 3.20e-01 77.5% 86.9%
5010136 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.52 41.0 3.27e-01 90.0% 67.0%
4679903 109.4.1.148 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › EST1_DNA_bind,EST1 0.52 45.0 2.77e-01 100.0% 22.4%
3414222 109.4.1.1134 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_INTS8_3 0.51 44.0 3.14e-01 100.0% 38.9%
4109408 321.1.1.7 ↗ a+b two layers › Glutamine synthetase-like › Glutamine synthetase/guanido kinase › Glutamine synthetase/guanido kinase › GCS2 0.51 44.0 2.92e-01 100.0% 80.8%
4139505 601.13.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › Flagellar export chaperone FliS › Flagellar export chaperone FliS › FliS 0.50 36.0 3.19e-01 78.8% 79.2%
D5 medium residues 616-758
PDB
Domain cluster: representative