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RNA-dependent_RNA_polymerase

Euk-Vir

Fig_fleck-associated_virus

RNA-dependent_RNA_polymerase__YP_004300302__Fig_fleck-associated_virus__548908

Identity

Accession:
YP_004300302 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

72.5 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 118-205
PDB
Domain cluster: representative
D2 medium residues 206-223_321-383_406-463
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5jxsA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.71 52.0 5.17e-01 87.1% 72.5%
1ra6A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.70 47.0 5.31e-01 80.6% 88.7%
6qwtA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.70 50.0 5.05e-01 87.1% 73.0%
3h5xA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.69 51.0 5.60e-01 83.5% 91.4%
7uinD01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.67 58.0 5.48e-01 93.5% 82.0%
1khvA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.63 48.0 4.97e-01 84.9% 84.6%
4zmuA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.55 43.0 4.23e-01 94.2% 76.1%
2ofhX00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 28.0 3.68e-01 71.2% 97.2%
1hi8A03 3.30.70.1600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 46.0 4.24e-01 91.4% 74.4%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5364 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.76 70.0 5.04e-01 100.0% 76.9%
1173784 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.76 71.0 5.11e-01 100.0% 78.0%
2541763 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.75 70.0 5.02e-01 100.0% 78.9%
None — 0.74 68.0 4.97e-01 100.0% 78.1%
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 0.71 61.0 4.68e-01 91.4% 52.8%
5369 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.71 66.0 4.43e-01 100.0% 76.0%
3353681 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 58.0 5.33e-01 91.4% 89.4%
3984781 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 0.62 53.0 5.09e-01 92.1% 86.9%
2033701 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 52.0 4.34e-01 94.2% 63.7%
D3 medium residues 224-257_287-320
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1sw6A00 1.25.40.20 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ankyrin repeat-containing domain 0.64 35.0 2.38e-01 80.9% 14.6%
2nscA01 3.30.70.1050 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Trigger factor ribosome-binding domain 0.63 53.0 5.06e-01 98.5% 80.8%
1mhyG01 1.20.1280.10 Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 1 0.61 33.0 3.39e-01 76.5% 52.9%
3iylB02 1.10.2050.10 Mainly Alpha › Orthogonal Bundle › Protein mu-1, chain B, domain 3 › Protein mu-1, chain B, domain 3 0.60 47.0 3.91e-01 97.1% 45.5%
4ragA02 1.10.10.430 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Phosphatase 2C, C-terminal domain suprefamily 0.59 36.0 3.67e-01 75.0% 61.8%
2rn7A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 32.0 3.26e-01 75.0% 53.0%
1gcvA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.58 45.0 3.62e-01 95.6% 41.4%
2k85A00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.57 36.0 3.67e-01 77.9% 66.2%
4gf0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.57 40.0 3.42e-01 75.0% 49.6%
2ra1A03 1.20.58.770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 32.0 3.37e-01 77.9% 60.3%
3crmA02 1.10.287.890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain 0.55 47.0 4.41e-01 97.1% 97.6%
2i1yA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.55 46.0 3.07e-01 94.1% 98.3%
4ri6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 36.0 3.05e-01 73.5% 38.7%
1cqxA01 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.55 44.0 3.47e-01 91.2% 40.7%
2hxoA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.54 46.0 3.74e-01 100.0% 94.4%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.54 39.0 3.93e-01 79.4% 76.5%
4b1bA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 45.0 2.81e-01 98.5% 18.3%
6d2qA02 1.20.80.10 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.53 40.0 3.54e-01 83.8% 91.3%
3h0gA05 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.51 43.0 3.46e-01 97.1% 57.5%
1w36C06 1.10.10.990 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.50 32.0 3.17e-01 94.1% 56.9%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3685074 101.7.1.1 ↗ alpha arrays › HTH › DEK-C › DEK-C › DEK_C 0.76 44.0 4.66e-01 86.8% 65.0%
3591354 1128.1.1.0 ↗ alpha bundles › LYR protein › LYR protein › LYR protein 0.61 41.0 4.52e-01 92.6% 87.3%
3519127 4979.2.1.1 ↗ alpha arrays › C-terminal domain of Hypothetical protein MPN330-like › XRN2-binding domain (XTBD) › XRN2-binding domain (XTBD) › XTBD 0.59 36.0 3.50e-01 94.1% 51.2%
3672080 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.58 50.0 4.33e-01 100.0% 72.7%
3270548 101.1.1.3 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-binding 0.58 35.0 3.68e-01 86.8% 61.7%
3653854 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.57 40.0 3.89e-01 73.5% 78.7%
3601305 558.1.1.0 ↗ alpha duplicates or obligate multimers › Lis-homology dimerization domain › Lis-homology dimerization domain › Lis-homology dimerization domain 0.56 33.0 3.29e-01 75.0% 54.8%
3741114 223.2.1.29 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › DENND11 0.55 40.0 3.11e-01 94.1% 33.8%
3886874 189.1.1.2 ↗ alpha bundles › GTPase activation domain, GAP › GTPase activation domain, GAP › GTPase activation domain, GAP › RhoGAP 0.54 38.0 3.08e-01 75.0% 65.2%
3834967 5063.1.1.1 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › PSI_PSAK 0.54 45.0 4.02e-01 97.1% 93.0%
3672635 101.1.1.295 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_70 0.53 32.0 3.18e-01 86.8% 53.3%
3482901 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.52 40.0 3.87e-01 85.3% 95.0%
3390399 633.24.1.4 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › RIN1 0.52 42.0 3.79e-01 95.6% 62.9%
3607309 1189.1.1.2 ↗ alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG_B 0.52 42.0 2.76e-01 94.1% 87.0%
3547935 3204.1.1.0 ↗ extended segments › N-terminal regulatory segment of carnitine palmitoyltransferase 1A › N-terminal regulatory segment of carnitine palmitoyltransferase 1A › N-terminal regulatory segment of carnitine palmitoyltransferase 1A 0.51 42.0 3.71e-01 98.5% 65.5%
1870497 3271.1.1.1 ↗ alpha arrays › CdiA C-terminal nuclease domain › CdiA C-terminal nuclease domain › CdiA C-terminal nuclease domain › Ntox28 0.50 34.0 3.09e-01 72.1% 55.4%
3497752 101.1.1.67 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-bind_6 0.50 32.0 3.33e-01 75.0% 69.2%
D4 medium residues 258-286_384-405
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vclA03 3.30.1750.10 Alpha Beta › 2-Layer Sandwich › hemolytic lectin cel-iii, domain 3 › Hemolytic lectin CEL-III, C-terminal domain 0.57 44.0 3.24e-01 88.2% 77.7%
D5 medium residues 482-594
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4g12A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.52 44.0 4.06e-01 93.8% 83.9%
1kblA05 1.20.80.30 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.50 28.0 3.13e-01 79.6% 67.4%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3697948 109.4.1.356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans 0.57 47.0 3.10e-01 90.3% 33.6%
4019131 611.3.1.0 ↗ alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.54 45.0 3.88e-01 89.4% 90.9%
3172167 604.6.1.2 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › ANTH 0.53 41.0 3.72e-01 82.3% 96.1%
3628258 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 43.0 3.88e-01 92.0% 83.5%
3429029 611.3.1.17 ↗ alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › TELO2_ARM 0.50 44.0 3.97e-01 100.0% 70.0%