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RNA-dependent_RNA_polymerase

Euk-Vir

Hubei_mosquito_virus_3

RNA-dependent_RNA_polymerase__YP_009337789__Hubei_mosquito_virus_3__1922927

Identity

Accession:
YP_009337789 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

66.5 mean pLDDT

Cluster

View cluster (32 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 1-95
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3iqcA00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.70 58.0 5.37e-01 89.5% 98.3%
1v9mA03 1.20.1690.10 Mainly Alpha › Up-down Bundle › V-type ATP synthase subunit C fold › V-type ATP synthase subunit C domain 0.68 51.0 5.09e-01 77.9% 97.9%
3vbbE01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.63 46.0 4.25e-01 81.1% 60.5%
7d5qA01 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.62 50.0 4.06e-01 88.4% 95.1%
4zvaA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.61 42.0 3.64e-01 71.6% 65.1%
1hxaA02 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.60 53.0 3.61e-01 100.0% 51.8%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.60 51.0 4.36e-01 92.6% 76.3%
4uurA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.59 41.0 3.76e-01 96.8% 54.0%
3zh9B03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.58 49.0 4.49e-01 93.7% 73.0%
3wa8B00 1.10.520.40 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › CRISPR-associated protein Cse2 0.57 50.0 4.16e-01 98.9% 100.0%
7p2yd01 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.56 44.0 4.41e-01 87.4% 93.9%
1bgfA00 1.10.532.10 Mainly Alpha › Orthogonal Bundle › Transcription Factor, Stat-4 › STAT transcription factor, N-terminal domain 0.55 47.0 4.35e-01 98.9% 71.8%
3owaB04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.54 36.0 3.05e-01 78.9% 41.4%
4wd2A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.54 40.0 3.42e-01 78.9% 86.0%
5tqbB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 48.0 3.28e-01 100.0% 45.5%
6nhiA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.52 41.0 2.85e-01 86.3% 33.0%
7ckaA01 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.51 41.0 3.32e-01 90.5% 61.4%
2h21A02 3.90.1420.10 Alpha Beta › Alpha-Beta Complex › set domain protein methyltransferase, domain 2 › Rubisco LSMT, substrate-binding domain 0.51 43.0 3.61e-01 92.6% 70.3%
2a0uB01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.51 46.0 3.87e-01 100.0% 71.9%
1escA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.51 40.0 2.86e-01 86.3% 37.1%
3uj9A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 44.0 3.21e-01 95.8% 94.6%
2pfdA03 1.20.120.680 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Formiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle 0.51 44.0 3.44e-01 95.8% 81.8%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3684369 601.13.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Flagellar export chaperone FliS › Flagellar export chaperone FliS 0.67 58.0 5.52e-01 94.7% 100.0%
3645325 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.65 43.0 3.83e-01 81.1% 48.1%
4292119 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.63 52.0 4.08e-01 89.5% 89.0%
4388053 138.1.1.5 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA_pol3_gamma3 0.62 51.0 4.63e-01 92.6% 67.2%
3590682 138.1.1.5 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA_pol3_gamma3 0.62 52.0 4.39e-01 93.7% 55.5%
5050478 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 0.61 51.0 3.73e-01 89.5% 79.2%
3526105 604.3.1.18 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › PF27519 0.61 42.0 4.32e-01 88.4% 74.4%
4954446 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.61 35.0 3.84e-01 77.9% 69.3%
4153328 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 0.61 50.0 3.95e-01 89.5% 87.5%
4531337 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.60 41.0 3.86e-01 77.9% 58.3%
4305487 5050.1.1.22 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1_like 0.60 47.0 3.64e-01 83.2% 89.0%
4145434 138.1.1.6 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA_pol3_delt_C 0.60 51.0 4.72e-01 93.7% 75.0%
3891431 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 0.59 44.0 3.30e-01 80.0% 90.5%
3969344 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 0.58 43.0 3.50e-01 78.9% 93.2%
4626667 138.1.1.9 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA_pol3_delta_C 0.58 50.0 4.54e-01 93.7% 72.6%
4031434 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.57 38.0 4.00e-01 88.4% 76.5%
3917484 5050.1.1.1 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.56 42.0 3.09e-01 78.9% 56.4%
3962942 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.56 40.0 3.44e-01 78.9% 47.3%
4354060 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.56 42.0 3.79e-01 84.2% 59.2%
4033064 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.56 41.0 3.25e-01 77.9% 55.5%
4985818 1079.1.1.8 ↗ alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › LysE 0.55 49.0 3.82e-01 97.9% 96.6%
3692803 1147.1.1.3 ↗ alpha bundles › RNA polymerase II elongation factor ELL2 C-terminal domain › RNA polymerase II elongation factor ELL2 C-terminal domain › RNA polymerase II elongation factor ELL2 C-terminal domain › CNNM 0.55 42.0 3.98e-01 81.1% 68.7%
3492369 622.4.1.21 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › Frag1 0.55 45.0 4.13e-01 86.3% 92.5%
3170301 5059.1.1.5 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › UAA 0.54 47.0 3.32e-01 100.0% 73.0%
3396357 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.54 45.0 4.69e-01 96.8% 98.9%
3804219 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.53 38.0 3.92e-01 78.9% 77.8%
3263961 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.52 44.0 3.58e-01 91.6% 97.1%
5065235 101.1.2.738 ↗ alpha arrays › HTH › HTH › winged helix domain › Vir_act_alpha_C 0.52 47.0 3.76e-01 100.0% 50.8%
3765458 150.3.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › Hormone_1 0.51 42.0 3.30e-01 89.5% 65.7%
3534658 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.50 42.0 3.52e-01 90.5% 78.8%
3912386 150.3.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › Hormone_1 0.50 43.0 3.40e-01 95.8% 67.8%
3253283 192.5.1.14 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.50 45.0 4.52e-01 96.8% 95.8%
D2 medium residues 96-120_142-166_191-245_318-333
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zxhA00 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.50 18.0 2.54e-01 87.6% 62.5%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.63 48.0 3.42e-01 79.3% 50.7%
3598902 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 0.63 48.0 3.32e-01 79.3% 51.8%
4071235 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 0.62 47.0 3.09e-01 79.3% 39.8%
4516798 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 0.62 47.0 3.16e-01 79.3% 44.2%
3615272 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 0.62 48.0 3.35e-01 81.8% 57.7%
4882475 210.1.1.0 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits 0.51 22.0 2.56e-01 99.2% 53.5%
D3 medium residues 121-141_284-317
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ib0A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.68 50.0 3.80e-01 80.0% 88.9%
4c91A02 3.20.20.520 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosyl hydrolase family 115 0.61 49.0 3.15e-01 92.7% 28.1%
2p0vA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.58 50.0 2.98e-01 100.0% 42.9%
1dq3A02 3.30.160.90 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.53 43.0 3.94e-01 96.4% 67.1%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3647808 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 53.0 4.29e-01 100.0% 67.8%
3700502 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.61 51.0 3.82e-01 100.0% 77.3%
5024001 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.60 50.0 4.24e-01 100.0% 94.0%
3849002 109.4.1.77 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › AAR2 0.60 46.0 3.34e-01 90.9% 72.3%
3613133 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.60 46.0 4.08e-01 87.3% 85.9%
3280650 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.58 47.0 3.17e-01 100.0% 34.2%
3724761 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.58 45.0 4.24e-01 87.3% 82.9%
3727680 3447.1.1.4 ↗ alpha bundles › Isoprenylcysteine carboxyl methyltransferase (ICMT) › Isoprenylcysteine carboxyl methyltransferase (ICMT) › Isoprenylcysteine carboxyl methyltransferase (ICMT) › PEMT 0.56 38.0 2.47e-01 72.7% 33.8%
4341411 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.55 45.0 4.19e-01 96.4% 87.8%
D4 medium residues 246-283_334-413
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337087__Hubei_narna-like_virus_4__1922958__D375-415_481-588