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RNA-dependent_RNA_polymerase

Euk-Vir

Hubei_narna-like_virus_19

RNA-dependent_RNA_polymerase__YP_009337792__Hubei_narna-like_virus_19__1922949

Identity

Accession:
YP_009337792 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

76.2 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 high residues 3-145
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7dl9A01 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.52 37.0 3.38e-01 73.4% 84.0%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.51 35.0 3.99e-01 87.4% 93.5%
4zudA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.51 42.0 3.46e-01 87.4% 91.4%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5020611 3352.1.1.0 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain 0.52 44.0 3.34e-01 95.1% 87.0%
3668980 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.51 36.0 3.72e-01 71.3% 84.4%
3927191 633.23.1.4 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Claudin_2 0.51 37.0 3.10e-01 74.1% 85.5%
4015031 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 0.51 45.0 3.11e-01 97.2% 85.2%
3969948 611.4.1.2 ↗ alpha bundles › N-cbl like › PG0775 C-terminal domain-like › PG0775 C-terminal domain-like › Acyl-CoA_dh_C 0.50 35.0 3.66e-01 72.0% 97.0%
4840917 5067.1.1.5 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Sterol-sensing 0.50 43.0 3.82e-01 95.8% 67.3%
D2 medium residues 147-171_205-309_382-399
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337775__Hubei_narna-like_virus_21__1922952__D110-165_177-251_312-348
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mukA02 3.90.1850.10 Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 0.57 50.0 3.44e-01 95.3% 58.6%
2uvaG03 3.30.70.3320 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 26.0 2.92e-01 70.9% 61.1%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4019374 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 0.65 60.0 4.32e-01 100.0% 74.6%
2850105 304.48.1.19 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Bunya_RdRp 0.64 53.0 4.36e-01 87.8% 84.2%
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 0.63 58.0 4.22e-01 100.0% 62.1%
4152428 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 0.61 49.0 3.63e-01 83.1% 54.9%
4497954 304.48.1.73 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1, RVT_N 0.61 48.0 3.74e-01 83.1% 70.6%
3589612 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 0.60 48.0 3.64e-01 83.1% 65.5%
5018583 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 0.59 47.0 3.66e-01 83.1% 66.3%
3097450 304.48.1.12 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mononeg_RNA_pol 0.59 49.0 3.56e-01 88.5% 77.7%
4647653 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.59 41.0 2.94e-01 70.3% 87.8%
3173834 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 0.58 46.0 3.30e-01 83.1% 43.4%
4004424 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 45.0 3.35e-01 83.1% 57.6%
5368 304.48.1.23 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_5 0.57 50.0 3.66e-01 95.3% 75.5%
3945039 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 45.0 3.43e-01 83.1% 54.2%
223786 304.48.1.16 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_4 0.55 48.0 3.74e-01 95.3% 74.3%
4901747 304.48.1.76 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › PF29845 0.53 43.0 3.51e-01 83.1% 68.0%
5029718 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 0.53 42.0 3.19e-01 83.1% 54.4%
5002351 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 0.53 42.0 3.15e-01 83.1% 48.8%
5078830 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 0.53 41.0 3.40e-01 81.8% 72.8%
4138932 304.48.1.72 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_N 0.53 38.0 3.00e-01 74.3% 56.0%
4937067 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 0.51 40.0 3.29e-01 83.1% 62.3%
4068028 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 0.50 39.0 3.17e-01 83.1% 66.6%
D3 medium residues 172-204_310-381_400-467
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009330065__Hubei_narna-like_virus_18__1922948__D96-147_214-259_290-363
D4 medium residues 468-510
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1v3eA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.59 49.0 2.83e-01 100.0% 9.7%
2wb7A02 2.60.40.2050 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 48.0 3.36e-01 100.0% 59.4%
3dsbA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 41.0 3.21e-01 100.0% 34.7%
4q52A00 2.60.40.3910 Mainly Beta › Sandwich › Immunoglobulin-like › Inclusion body protein 0.57 46.0 3.20e-01 100.0% 48.0%
1xezA03 6.20.40.20 Special › Other non-globular › Porin MspA ribbon fold › Leukocidin/Hemolysin toxin, pre-stem domain 0.55 42.0 4.10e-01 88.4% 79.2%
4lb8A02 2.60.40.3900 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 46.0 3.23e-01 100.0% 54.7%
2ougA00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.52 41.0 3.05e-01 100.0% 31.2%
2cc3A00 3.10.450.230 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › VirB8 protein 0.51 43.0 3.08e-01 100.0% 36.1%
8ainB01 3.10.450.250 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › S. aureus uracil DNA glycosylase inhibitor 0.51 40.0 3.22e-01 97.7% 47.6%
1uunA02 2.10.300.10 Mainly Beta › Ribbon › Porin MspA ribbon fold › Porin MspA ribbon domain 0.50 35.0 3.35e-01 76.7% 65.4%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3606648 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.63 48.0 3.60e-01 90.7% 40.0%
5070582 815.1.1.0 ↗ a+b two layers › Chromosomal protein MC1 › Chromosomal protein MC1 › Chromosomal protein MC1 0.60 48.0 4.05e-01 100.0% 56.5%
3203972 810.1.1.0 ↗ a+b two layers › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) 0.59 40.0 3.10e-01 100.0% 27.8%
3440037 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.58 48.0 2.83e-01 100.0% 11.4%
4946045 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.56 48.0 4.12e-01 100.0% 64.3%
3479291 5.1.5.67 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › Beta-prop_WDR19_2nd 0.55 43.0 2.63e-01 100.0% 12.1%
5014841 282.1.1.1 ↗ a+b duplicates or obligate multimers › CBS-domain › CBS-domain › CBS-domain › CBS 0.55 44.0 3.15e-01 97.7% 48.4%
3273636 328.1.1.0 ↗ a+b two layers › IF3-like › AlbA-like › AlbA-like 0.55 44.0 4.06e-01 100.0% 83.1%
4930176 282.1.1.1 ↗ a+b duplicates or obligate multimers › CBS-domain › CBS-domain › CBS-domain › CBS 0.54 43.0 2.75e-01 100.0% 71.7%
4978408 247.1.1.12 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B_3 0.54 41.0 2.71e-01 95.3% 50.0%
3484178 304.47.1.0 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain 0.53 41.0 3.06e-01 100.0% 40.0%
3967397 7503.1.1.8 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › DUF4136 0.53 41.0 3.02e-01 100.0% 52.7%
4963626 4004.1.1.3 ↗ beta sandwiches › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › NAD_kinase_C 0.53 37.0 2.67e-01 86.0% 21.9%
3601915 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.52 35.0 2.29e-01 76.7% 67.4%
3726495 7579.1.1.44 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_6 0.52 39.0 2.47e-01 95.3% 13.8%
3626243 5.1.4.277 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, Beta-prop_EIPR1 0.52 41.0 2.41e-01 90.7% 10.4%
4961086 282.1.1.1 ↗ a+b duplicates or obligate multimers › CBS-domain › CBS-domain › CBS-domain › CBS 0.51 40.0 2.88e-01 97.7% 48.2%
3666679 831.1.1.2 ↗ a+b two layers › NSFL1 (p97 ATPase) cofactor p47, SEP domain › NSFL1 (p97 ATPase) cofactor p47, SEP domain › NSFL1 (p97 ATPase) cofactor p47, SEP domain › Spt20_SEP 0.51 39.0 3.26e-01 100.0% 83.7%
3593467 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 42.0 2.50e-01 100.0% 12.3%
5045394 282.1.1.1 ↗ a+b duplicates or obligate multimers › CBS-domain › CBS-domain › CBS-domain › CBS 0.50 40.0 2.85e-01 97.7% 50.6%
3708096 3926.1.1.0 ↗ alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D 0.50 39.0 2.86e-01 97.7% 62.6%