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RNA-dependent_RNA_polymerase

Euk-Vir

Wheat_yellow_dwarf_virus-GPV

RNA-dependent_RNA_polymerase__YP_003029839__Wheat_yellow_dwarf_virus-GPV__572239

Identity

Accession:
YP_003029839 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

76.5 mean pLDDT

Cluster

View cluster (38 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 112-201
PDB
D2 medium residues 202-223_311-395
PDB
Domain cluster: rep: hypothetical_protein_1__YP_009337259__Shuangao_sobemo-like_virus_2__1923475__D83-106_193-282
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02122.22 best Peptidase_S39 111.6 5.60e-32 80.4% 42.9%
D3 medium residues 224-310
PDB
Domain cluster: rep: hypothetical_protein__YP_009825042__Birds-foot_trefoil_enamovirus_1__2283314__D329-413
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02122.22 best Peptidase_S39 106.9 1.50e-30 100.0% 42.4%
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zyoA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.84 75.0 7.66e-01 95.4% 98.8%
3su0A01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.75 53.0 4.82e-01 96.6% 56.2%
2o8mB01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.75 53.0 5.96e-01 96.6% 95.5%
3k6yA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.75 62.0 6.10e-01 96.6% 82.6%
5hmaA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.75 64.0 6.43e-01 96.6% 92.0%
2z9iC01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.71 61.0 6.01e-01 95.4% 87.0%
1l1jA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.69 62.0 5.55e-01 96.6% 87.3%
1lvmA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.69 62.0 5.84e-01 98.9% 82.1%
4rqyA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.69 63.0 5.58e-01 100.0% 72.4%
1ntpA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.68 61.0 5.78e-01 98.9% 89.3%
5lpeB02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.67 59.0 5.83e-01 100.0% 91.4%
2gk6A02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.65 51.0 5.23e-01 88.5% 88.0%
2sfaA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.63 56.0 5.56e-01 98.9% 98.9%
2wv9A01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.61 47.0 3.84e-01 83.9% 45.3%
4b6eB01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.60 46.0 3.60e-01 86.2% 36.1%
2xzlA02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.60 44.0 4.62e-01 87.4% 87.3%
4rt0A00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.59 52.0 4.81e-01 96.6% 89.9%
4m9fA00 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.58 48.0 3.74e-01 94.3% 40.0%
6x4tA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 41.0 4.22e-01 75.9% 100.0%
1s4iA00 2.60.40.200 Mainly Beta › Sandwich › Immunoglobulin-like › Superoxide dismutase, copper/zinc binding domain 0.57 48.0 4.02e-01 92.0% 98.0%
2vs7A02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.55 40.0 4.22e-01 92.0% 88.5%
3zduA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.55 41.0 4.31e-01 88.5% 90.8%
6ahuH01 3.30.70.3250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribonuclease P, Pop5 subunit 0.54 38.0 3.72e-01 72.4% 90.5%
3goxA02 3.30.60.130 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.54 31.0 3.69e-01 77.0% 90.7%
3fzqA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.54 42.0 3.81e-01 82.8% 94.8%
3uimA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 39.0 3.92e-01 87.4% 76.4%
1b7tA02 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.53 28.0 3.36e-01 94.3% 82.7%
2osxA01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 39.0 3.74e-01 92.0% 68.7%
3dtdD00 2.60.40.1880 Mainly Beta › Sandwich › Immunoglobulin-like › Invasion associated locus B (IalB) protein 0.52 44.0 3.79e-01 97.7% 82.1%
1zysA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 43.0 4.18e-01 92.0% 83.2%
1dn0D02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 38.0 3.77e-01 80.5% 95.7%
4l68A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 39.0 3.62e-01 87.4% 63.6%
4v1al00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.50 40.0 3.46e-01 85.1% 57.9%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2710030 1.1.5.12 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_S39 0.85 79.0 5.98e-01 100.0% 85.9%
3452728 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.73 68.0 5.03e-01 100.0% 42.4%
4205419 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.73 67.0 4.86e-01 100.0% 44.8%
3957702 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.73 64.0 5.50e-01 100.0% 61.5%
3989070 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.72 66.0 4.84e-01 100.0% 50.5%
3435448 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.69 63.0 4.55e-01 100.0% 38.7%
3454710 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.69 63.0 4.62e-01 100.0% 85.0%
3280223 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.67 60.0 4.65e-01 100.0% 49.7%
3277840 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.65 58.0 4.42e-01 100.0% 44.6%
3278337 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.65 58.0 4.47e-01 100.0% 92.3%
22055 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.64 57.0 4.44e-01 100.0% 48.7%
3950458 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.63 57.0 4.49e-01 100.0% 93.9%
3992051 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.57 44.0 4.15e-01 83.9% 95.2%
3531830 11.1.1.363 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_3 0.56 42.0 3.95e-01 81.6% 86.4%
4382401 1.1.7.100 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PGBA_N 0.56 45.0 4.62e-01 89.7% 90.6%
3778889 11.1.1.108 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.56 41.0 3.60e-01 80.5% 67.9%
3197931 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.55 42.0 3.66e-01 81.6% 100.0%
3575268 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.55 41.0 3.90e-01 81.6% 84.5%
3299797 4.1.1.306 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_VIII-1_N 0.55 30.0 3.41e-01 93.1% 71.7%
4604674 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.55 39.0 3.36e-01 75.9% 95.2%
3842044 11.1.1.108 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.55 39.0 3.61e-01 77.0% 62.5%
1002459 378.1.1.13 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › His_Me_b4a2 0.53 31.0 3.73e-01 82.8% 96.2%
3252416 304.57.1.1 ↗ a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.52 38.0 3.50e-01 78.2% 68.3%
4970376 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.52 38.0 4.10e-01 78.2% 94.7%
4192947 101.1.2.16 ↗ alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.52 42.0 3.49e-01 90.8% 98.2%
3228278 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 28.0 3.18e-01 93.1% 67.7%
4218945 101.1.2.16 ↗ alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.51 43.0 3.86e-01 94.3% 94.4%
3385440 1.1.8.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain 0.50 36.0 3.73e-01 75.9% 95.0%
D4 medium residues 567-617_772-792
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1p65A00 6.10.140.90 Special › Helix non-globular › Helix Hairpins › 0.67 29.0 3.27e-01 88.9% 52.6%
3mk7C01 6.10.280.130 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 47.0 4.34e-01 86.1% 66.0%
1loxA01 1.20.245.10 Mainly Alpha › Up-down Bundle › Lipoxygenase-1; domain 5 › Lipoxygenase-1; Domain 5 0.54 43.0 2.74e-01 90.3% 84.8%
2kjwA00 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.51 25.0 2.28e-01 73.6% 31.2%
4cllA01 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.50 43.0 3.18e-01 100.0% 66.2%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4238391 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.79 34.0 2.83e-01 81.9% 26.1%
5038348 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.67 54.0 4.30e-01 86.1% 77.9%
4023214 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.65 56.0 4.20e-01 93.1% 77.6%
3506095 167.1.1.1 ↗ alpha arrays › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal_S7 0.63 42.0 3.24e-01 90.3% 31.8%
4318691 5061.1.1.1 ↗ alpha complex topology › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › Preprotein translocase SecY subunit › SecY 0.60 49.0 3.06e-01 91.7% 16.4%
3853449 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.58 44.0 4.05e-01 83.3% 94.7%
4163347 3681.1.1.0 ↗ a+b complex topology › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit 0.57 49.0 4.15e-01 95.8% 60.8%
5000735 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 45.0 3.34e-01 86.1% 42.3%
3221141 188.1.1.1 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.55 49.0 3.35e-01 100.0% 89.8%
3244912 206.1.1.44 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › DUF1679 0.55 50.0 3.05e-01 100.0% 44.9%
3727157 611.7.1.0 ↗ alpha bundles › N-cbl like › Mixed lineage kinase domain-like (MLKL) N-terminal domain › Mixed lineage kinase domain-like (MLKL) N-terminal domain 0.54 43.0 3.59e-01 86.1% 51.2%
4023956 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.53 45.0 3.73e-01 94.4% 89.2%
3614726 4357.1.1.0 ↗ beta barrels › WWE domain › WWE domain › WWE domain 0.51 45.0 3.75e-01 94.4% 91.7%
3171717 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.51 43.0 3.01e-01 95.8% 81.9%
1152673 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.51 36.0 3.20e-01 88.9% 50.9%
3228072 188.1.1.1 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.51 45.0 3.08e-01 100.0% 98.5%
D5 medium residues 618-699_793-817
PDB
Domain cluster: rep: replicase_polyprotein__YP_009465710__Pepper_enamovirus__2073163__D698-776_892-917
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 32.2 7.90e-08 69.2% 15.9%
D6 medium residues 700-771_818-838
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337098__Changjiang_polero-like_virus_1__1922799__D1-82_112-138
D7 medium residues 1020-1077
PDB
Domain cluster: rep: putative_protein_P2__YP_001931931__Tobacco_vein_distorting_virus__192203__D1031-1055_1057-1076_1079-1084