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RNA-dependent_RNA_polymerase

Euk-Vir

Shahe_narna-like_virus_2

RNA-dependent_RNA_polymerase__YP_009336615__Shahe_narna-like_virus_2__1923430

Identity

Accession:
YP_009336615 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

61.7 mean pLDDT

Cluster

View cluster (39 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 6-83
PDB
D2 medium residues 84-232
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4e40A00 1.20.1260.80 Mainly Alpha › Up-down Bundle › Ferritin › 0.65 36.0 3.01e-01 100.0% 32.2%
3h7iA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.60 32.0 4.27e-01 99.3% 98.7%
6cnzF00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.60 43.0 4.26e-01 100.0% 69.0%
4ceiA03 6.10.250.2380 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.59 40.0 4.48e-01 98.7% 89.3%
1r0dA00 1.20.1410.10 Mainly Alpha › Up-down Bundle › I/LWEQ domain › I/LWEQ domain 0.59 47.0 4.37e-01 84.6% 92.7%
8gy0A01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.59 40.0 3.26e-01 87.9% 36.3%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.57 38.0 4.23e-01 96.6% 86.0%
3lmfA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.57 37.0 4.22e-01 96.6% 88.1%
2wy4A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.57 39.0 4.06e-01 99.3% 74.8%
3ajmB02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.56 33.0 3.49e-01 87.2% 64.7%
7e4mA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.55 41.0 3.39e-01 76.5% 55.6%
3qsgA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.55 32.0 3.62e-01 94.0% 74.8%
2zxqA06 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.54 26.0 3.56e-01 85.9% 97.0%
1h6gA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.54 35.0 3.79e-01 91.3% 77.4%
1sj8A02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.53 40.0 4.28e-01 98.7% 94.3%
3wecA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.52 42.0 3.08e-01 84.6% 41.4%
7watB02 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.52 41.0 3.21e-01 81.9% 53.1%
1xioA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.52 43.0 3.85e-01 89.3% 76.0%
1binA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.52 35.0 3.65e-01 95.3% 72.0%
1h97A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 38.0 3.89e-01 100.0% 79.6%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5070002 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.58 31.0 3.32e-01 88.6% 56.9%
4364069 607.1.1.1 ↗ alpha arrays › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › PEP-utilisers_N 0.58 42.0 4.54e-01 99.3% 89.6%
3212065 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.54 40.0 4.24e-01 99.3% 84.4%
4283166 604.5.1.31 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › TRAM_LAG1_CLN8 0.53 41.0 3.40e-01 82.6% 94.6%
4027586 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.53 35.0 3.10e-01 81.9% 44.4%
4028049 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.52 47.0 3.84e-01 100.0% 95.9%
4952627 142.1.1.14 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › NiFe_hyd_3_EhaA 0.52 31.0 3.86e-01 77.2% 100.0%
4978846 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.52 38.0 4.24e-01 98.7% 97.4%
4967345 5069.1.1.15 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cytochrom_C_asm 0.51 36.0 3.76e-01 83.9% 78.3%
D3 medium residues 233-280_401-449_497-549
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1pu1A00 3.30.300.100 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › MTH677-like 0.51 26.0 3.21e-01 100.0% 78.0%
3mk7C01 6.10.280.130 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 23.0 2.83e-01 92.0% 67.0%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.78 72.0 5.38e-01 100.0% 67.2%
3792091 304.48.1.25 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 0.73 55.0 4.13e-01 77.3% 58.6%
3877925 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 0.72 66.0 4.84e-01 99.3% 69.6%
3789227 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 0.71 58.0 4.53e-01 86.7% 77.4%
3708776 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 0.61 52.0 3.97e-01 89.3% 69.8%
3236725 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 0.57 48.0 3.94e-01 88.7% 57.7%
4884617 4001.1.1.4 ↗ a+b duplicates or obligate multimers › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › Cullin_AB 0.54 24.0 2.99e-01 83.3% 63.5%
D4 medium residues 321-400
PDB
D5 medium residues 450-496_550-667
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337087__Hubei_narna-like_virus_4__1922958__D375-415_481-588
D6 medium residues 846-864_960-1011
PDB