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RNA-dependent_RNA_polymerase

Euk-Vir

Trichoderma_atroviride_mycovirus

RNA-dependent_RNA_polymerase__YP_009342055__Trichoderma_atroviride_mycovirus__1934322

Identity

Accession:
YP_009342055 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

81.0 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 754-892
PDB
D2 medium residues 8-115
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fdiA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.64 58.0 3.93e-01 100.0% 74.6%
1aukA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.63 57.0 3.88e-01 100.0% 76.6%
7aj0A01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.61 56.0 3.77e-01 100.0% 78.2%
1k77A00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.60 41.0 3.11e-01 70.4% 86.1%
2gsoA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.58 52.0 3.89e-01 100.0% 83.2%
2w5qA02 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.57 51.0 3.69e-01 100.0% 75.2%
1lrzA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 39.0 3.55e-01 74.1% 82.5%
6fdfA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 37.0 3.05e-01 70.4% 62.1%
3b6hA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.54 42.0 2.82e-01 85.2% 73.8%
2w00A01 3.90.1570.50 Alpha Beta › Alpha-Beta Complex › tt1808, chain A › 0.53 45.0 3.84e-01 91.7% 98.8%
7kwdA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.52 47.0 3.27e-01 100.0% 70.0%
7yjmB01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.52 39.0 3.13e-01 83.3% 51.5%
1hdhA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.51 45.0 3.04e-01 100.0% 85.0%
3cniA00 3.40.1710.10 Alpha Beta › 3-Layer(aba) Sandwich › abc type-2 transporter like fold › abc type-2 transporter like domain 0.51 35.0 3.23e-01 92.6% 53.1%
2i8dA01 3.90.1150.200 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.50 30.0 3.33e-01 76.9% 76.5%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3508213 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.69 48.0 4.01e-01 70.4% 67.2%
4599467 4126.1.1.5 a/b three-layered sandwiches › beta-carbonic anhydrase-like › beta-carbonic anhydrase › beta-carbonic anhydrase › Pro_CA_2 0.65 46.0 4.02e-01 73.1% 79.3%
3274159 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.62 44.0 4.32e-01 73.1% 89.6%
3794616 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.58 44.0 3.24e-01 82.4% 90.8%
4949827 7518.1.1.6 a/b three-layered sandwiches › PK C-terminal domain-like › PK C-terminal domain-like › PK C-terminal domain-like › DacZ_A 0.58 47.0 4.71e-01 95.4% 86.4%
3249997 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 50.0 4.29e-01 99.1% 97.8%
3753230 2004.1.1.139 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Torsin 0.56 47.0 3.46e-01 90.7% 60.4%
3723708 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.55 46.0 3.79e-01 89.8% 97.4%
4390140 149.1.1.1 alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.55 36.0 2.42e-01 90.7% 15.5%
None 0.55 47.0 3.48e-01 92.6% 68.0%
3700537 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.54 47.0 3.46e-01 91.7% 87.0%
2541233 3819.1.1.3 alpha complex topology › CRISPR-associated endonuclease Cas9 alpha-helical lobe › CRISPR-associated endonuclease Cas9 alpha-helical lobe › CRISPR-associated endonuclease Cas9 alpha-helical lobe › Cas9_a 0.54 39.0 2.68e-01 75.0% 40.9%
3728705 7516.1.1.63 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › CAP59_mtransfer 0.53 43.0 2.93e-01 89.8% 67.5%
4085823 513.1.1.1 a+b two layers › Obg GTP-binding protein C-terminal domain-like › Obg GTP-binding protein C-terminal domain › Obg GTP-binding protein C-terminal domain › DUF1967 0.51 32.0 3.53e-01 88.9% 80.0%
4280735 149.1.1.1 alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.51 40.0 2.70e-01 85.2% 65.1%
D3 medium residues 284-309_551-628
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ckwA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.67 49.0 4.74e-01 76.0% 69.8%
2efpA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.62 41.0 4.21e-01 75.0% 71.4%
6aqgD02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 39.0 2.76e-01 72.1% 89.5%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4965158 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.65 41.0 4.65e-01 76.9% 86.7%
4950395 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.64 46.0 4.60e-01 75.0% 74.5%
5040415 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.64 46.0 4.64e-01 75.0% 81.0%
4957408 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.64 45.0 4.58e-01 75.0% 80.0%
3194622 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.63 44.0 4.57e-01 74.0% 76.8%
4127140 310.1.1.2 a+b two layers › RRF/tRNA synthetase additional domain-like › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain › Arg_tRNA_synt_N 0.55 38.0 3.88e-01 70.2% 73.0%
3338702 206.1.1.20 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.50 30.0 2.40e-01 75.0% 30.5%
4955849 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.50 35.0 2.82e-01 72.1% 55.1%
D4 medium residues 310-326_384-417_467-550_629-645
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3besR03 6.10.140.1480 Special › Helix non-globular › Helix Hairpins › 0.72 26.0 4.32e-01 74.3% 91.1%
3a8tA02 1.10.287.890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain 0.58 31.0 3.57e-01 81.6% 69.4%
3k2jA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.57 28.0 3.15e-01 78.9% 57.9%
5u9nB00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.55 29.0 3.19e-01 78.9% 61.7%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.70 58.0 4.46e-01 87.5% 94.2%
3290011 3843.1.1.4 alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › PhaG_MnhG_YufB 0.62 33.0 4.16e-01 78.3% 84.2%
5034580 3843.1.1.4 alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › PhaG_MnhG_YufB 0.59 33.0 4.01e-01 77.0% 83.0%
3781981 633.1.1.1 alpha bundles › Bromodomain-like › Bromodomain › Bromodomain › Bromodomain 0.58 30.0 3.36e-01 76.3% 61.3%
3475233 5041.1.1.0 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.56 32.0 3.90e-01 84.2% 85.0%
4491397 3843.1.1.1 alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › Oxidored_q2 0.55 29.0 3.72e-01 80.9% 90.6%
3390061 5063.1.1.22 alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › LIN9_C 0.50 34.0 3.92e-01 80.3% 93.6%
D5 medium residues 911-996
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.75 30.0 3.54e-01 83.7% 53.2%
3ilkA02 1.10.8.590 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.54 31.0 3.48e-01 86.0% 72.1%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3832368 109.4.1.361 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › NPH3 0.59 31.0 2.78e-01 89.5% 36.7%
3379763 190.1.1.1 alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.57 43.0 4.47e-01 91.9% 86.3%
4959134 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 0.57 35.0 2.70e-01 91.9% 28.4%
4927740 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.56 30.0 2.63e-01 88.4% 34.6%
3597182 190.1.1.0 alpha arrays › HMG-box-like › HMG-box › HMG-box 0.56 38.0 3.99e-01 87.2% 76.2%
3174920 190.1.1.1 alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.53 42.0 4.32e-01 90.7% 88.2%
3794285 130.1.1.0 alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.52 35.0 3.73e-01 82.6% 78.7%
None 0.52 39.0 2.94e-01 80.2% 78.2%
2095477 1170.1.2.2 beta barrels › IL8-related › IL8-related › chemokine-related domain in glycoprotein L (gL) 0.52 34.0 2.91e-01 100.0% 41.7%
D6 medium residues 1046-1118
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1es2A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.67 47.0 3.22e-01 74.0% 45.0%
5aioA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.66 44.0 3.43e-01 75.3% 32.3%
3onkA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.65 51.0 4.19e-01 86.3% 80.3%
4u04B01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.64 42.0 3.95e-01 75.3% 55.7%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.62 49.0 4.87e-01 83.6% 92.0%
1hxiA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.62 44.0 3.89e-01 76.7% 74.1%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 47.0 4.59e-01 82.2% 78.2%
2yhsA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.60 44.0 4.04e-01 78.1% 59.8%
1tjcA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 42.0 3.85e-01 72.6% 90.5%
1g4uS01 1.20.120.260 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Virulence factor YopE uncharacterised domain 0.60 46.0 3.85e-01 83.6% 65.4%
3jsbA01 1.20.1440.300 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain 0.59 50.0 4.88e-01 95.9% 96.3%
2fu2A00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.59 50.0 4.90e-01 95.9% 96.2%
1go3F02 6.10.140.10 Special › Helix non-globular › Helix Hairpins › 0.59 37.0 4.28e-01 75.3% 97.9%
5jj6B01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.58 43.0 3.97e-01 79.5% 89.6%
1ks8A00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.57 48.0 3.03e-01 95.9% 45.5%
1ao0A01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.57 48.0 3.25e-01 97.3% 73.0%
4g1tA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.56 41.0 4.40e-01 83.6% 93.4%
3e7pA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.56 43.0 2.98e-01 83.6% 90.9%
2ifcA01 1.10.580.10 Mainly Alpha › Orthogonal Bundle › Citrate Synthase; domain 1 › Citrate Synthase, domain 1 0.56 45.0 3.12e-01 87.7% 61.1%
3ajfA00 1.20.1440.190 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tenuivirus movement protein 0.55 49.0 4.57e-01 100.0% 91.3%
3lltA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.55 41.0 2.92e-01 80.8% 84.3%
1b4pA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 44.0 3.91e-01 87.7% 75.2%
4dmbB00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.55 43.0 3.36e-01 93.2% 77.4%
3i4uA01 1.20.120.1080 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.53 40.0 3.66e-01 97.3% 61.9%
4f7nB01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.52 42.0 3.53e-01 93.2% 51.5%
3b34A03 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.52 39.0 3.12e-01 91.8% 37.2%
4ry2A01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 42.0 3.49e-01 95.9% 62.4%
4ip8A00 1.10.132.110 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Serum amyloid A protein 0.51 41.0 3.66e-01 89.0% 62.9%
3k8uA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 41.0 3.52e-01 95.9% 64.9%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3767823 109.4.1.2862 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1, TPR_6, TPR_8 0.66 50.0 3.32e-01 80.8% 30.9%
3740594 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.66 49.0 3.94e-01 86.3% 41.4%
3738259 592.2.1.0 alpha arrays › PWI domain-like › YugE-like › YugE-like 0.57 44.0 4.62e-01 86.3% 100.0%
3297949 592.7.1.2 alpha arrays › PWI domain-like › GIPC1 GH2 domain › GIPC1 GH2 domain › PWI 0.55 44.0 4.60e-01 94.5% 100.0%
3468254 592.2.1.0 alpha arrays › PWI domain-like › YugE-like › YugE-like 0.55 45.0 4.60e-01 93.2% 97.1%
3300095 592.1.1.1 alpha arrays › PWI domain-like › PWI domain › PWI domain › PWI 0.55 43.0 4.49e-01 95.9% 100.0%
5044421 592.2.1.0 alpha arrays › PWI domain-like › YugE-like › YugE-like 0.55 45.0 4.39e-01 94.5% 91.3%
3108769 604.12.1.1 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT 0.54 41.0 4.14e-01 82.2% 90.1%
3448417 109.4.1.297 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_EMC2 0.53 45.0 3.56e-01 95.9% 46.2%
4999825 4995.1.1.1 alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.51 43.0 3.93e-01 95.9% 86.0%