←Back to structures

RdRp

Euk-Vir

Hubei_permutotetra-like_virus_9

RdRp__YP_009337778__Hubei_permutotetra-like_virus_9__1923083

Identity

Accession:
YP_009337778 ↗
Protein ID:
RdRp
Kingdom:
euk

Quality

74.0 mean pLDDT

Cluster

View cluster (20 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 22-72_545-679
PDB
Domain cluster: rep: RdRp__YP_009337318__Hubei_permutotetra-like_virus_6__1923080__D29-60_540-665
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF22260.2 best Permu_RdRp_thumb 101.5 3.70e-29 57.0% 100.0%
D2 high residues 905-1002
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4wyqB00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.75 52.0 5.80e-01 77.6% 92.0%
2mdrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.70 56.0 5.71e-01 86.7% 87.2%
1yqzA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.68 41.0 4.00e-01 81.6% 54.6%
2gvhB02 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.67 40.0 3.76e-01 83.7% 48.7%
2v1oB00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.66 39.0 3.42e-01 83.7% 38.5%
2lrsA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.66 45.0 5.14e-01 70.4% 97.2%
1nhpA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.66 41.0 3.94e-01 81.6% 54.0%
2cduA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.66 41.0 3.92e-01 81.6% 54.0%
2bi0A02 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.65 39.0 3.44e-01 83.7% 40.8%
1gesA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.62 40.0 3.79e-01 80.6% 55.8%
3kh8B01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.61 37.0 3.24e-01 82.7% 37.7%
2hboA01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.61 35.0 3.19e-01 83.7% 40.6%
1pn2B01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.59 38.0 3.32e-01 83.7% 42.6%
7sulB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.57 40.0 2.83e-01 73.5% 29.3%
3loyA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.57 42.0 4.03e-01 77.6% 79.8%
2wraA00 2.60.120.400 Mainly Beta › Sandwich › Jelly Rolls › Calcium-mediated lectin 0.56 43.0 4.06e-01 82.7% 85.2%
6kghA02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.56 50.0 4.32e-01 100.0% 74.7%
3b7kB01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.55 39.0 3.42e-01 71.4% 65.7%
3ugfB02 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.55 42.0 3.49e-01 82.7% 67.8%
5df7A02 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 48.0 3.33e-01 100.0% 88.9%
1fx3B00 3.10.420.10 Alpha Beta › Roll › Bacterial Protein-export protein SecB › SecB-like 0.54 50.0 4.28e-01 100.0% 69.8%
5tfqA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 49.0 3.52e-01 100.0% 90.3%
6izcA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 49.0 3.57e-01 100.0% 92.4%
6pl6B01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 48.0 3.29e-01 100.0% 90.1%
3nqkA02 2.40.128.440 Mainly Beta › Beta Barrel › Lipocalin › Uncharacterised protein PF14274, DUF4361 0.53 42.0 3.56e-01 83.7% 90.6%
1sr9A02 3.30.160.270 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Alpha-isopropylmalate synthase LeuA, regulatory domain 0.53 43.0 3.76e-01 92.9% 70.7%
3eqvA02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.53 48.0 4.31e-01 100.0% 74.4%
4jf6A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 47.0 3.55e-01 100.0% 92.5%
2ebkA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.52 38.0 3.56e-01 77.6% 79.7%
3nwzB00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.52 36.0 3.14e-01 71.4% 90.7%
1kiaA01 3.30.46.10 Alpha Beta › 2-Layer Sandwich › Glycine N-methyltransferase; chain A, domain 1 › Glycine N-methyltransferase, chain A, domain 1 0.52 38.0 4.01e-01 77.6% 98.8%
1ukxA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.51 38.0 3.43e-01 78.6% 75.2%
2plqA00 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.51 40.0 2.83e-01 86.7% 59.7%
4kc5C03 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.51 41.0 2.91e-01 86.7% 82.2%
1xkzC00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 46.0 3.42e-01 100.0% 88.7%
4gn2A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.50 45.0 3.40e-01 100.0% 97.5%
2daxA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.50 37.0 3.32e-01 78.6% 82.3%
5o16B00 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.50 46.0 3.28e-01 99.0% 55.5%
3kg7B00 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.50 45.0 3.22e-01 99.0% 56.1%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3596299 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.74 56.0 5.48e-01 79.6% 91.4%
3710326 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.74 53.0 5.68e-01 79.6% 87.1%
3445028 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.74 55.0 5.96e-01 77.6% 96.2%
3704403 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.72 54.0 5.49e-01 77.6% 92.6%
3505181 330.1.1.5 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM 0.72 54.0 5.88e-01 78.6% 98.8%
4444614 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.72 54.0 5.95e-01 78.6% 96.2%
4472716 330.1.1.3 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dimer 0.70 52.0 4.68e-01 77.6% 63.8%
3481273 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.68 55.0 5.36e-01 84.7% 80.0%
3825504 330.1.1.5 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DND1_DSRM 0.68 50.0 5.25e-01 77.6% 84.4%
4936781 244.2.1.1 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Pyr_redox_dim 0.67 42.0 3.81e-01 81.6% 47.7%
3609908 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.66 51.0 4.90e-01 80.6% 82.7%
3939992 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.66 54.0 5.23e-01 87.8% 85.5%
5055184 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.66 45.0 4.81e-01 78.6% 82.4%
4982148 244.2.1.1 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Pyr_redox_dim 0.65 40.0 3.78e-01 81.6% 50.0%
3631773 222.1.1.4 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › 4HBT 0.65 37.0 3.06e-01 83.7% 30.9%
5001433 244.2.1.1 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Pyr_redox_dim 0.65 41.0 3.67e-01 81.6% 45.9%
3283651 222.1.1.9 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › MaoC_dehydrat_N 0.63 38.0 3.53e-01 83.7% 46.4%
3587843 244.2.1.1 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Pyr_redox_dim 0.63 41.0 3.73e-01 81.6% 49.6%
3785102 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.63 47.0 3.41e-01 100.0% 26.9%
3988052 244.2.1.1 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Pyr_redox_dim 0.63 39.0 3.63e-01 81.6% 49.2%
4873579 4019.1.1.3 ↗ alpha complex topology › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › Transpeptidase 0.62 40.0 4.42e-01 83.7% 83.3%
2640602 222.1.1.4 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › 4HBT 0.62 38.0 3.74e-01 86.7% 56.0%
3386467 7503.1.1.0 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain 0.61 54.0 4.76e-01 100.0% 98.7%
4945010 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.58 44.0 3.14e-01 81.6% 45.5%
3282536 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.58 41.0 4.41e-01 73.5% 91.3%
4954298 504.1.1.0 ↗ a+b two layers › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB 0.57 47.0 4.83e-01 100.0% 92.6%
4318546 504.1.1.1 ↗ a+b two layers › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB › Bacterial protein-export protein SecB › SecB 0.56 51.0 4.59e-01 100.0% 79.3%
3991810 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.56 41.0 3.61e-01 77.6% 70.7%
3973413 7503.1.1.0 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain 0.56 48.0 4.26e-01 100.0% 97.4%
4652220 223.3.1.3 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Transpeptidase 0.56 50.0 3.45e-01 100.0% 90.6%
3410646 223.1.1.71 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › VGCC_alpha2 0.56 38.0 2.83e-01 71.4% 47.7%
3993254 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 37.0 4.10e-01 75.5% 85.0%
3966462 223.3.1.3 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Transpeptidase 0.55 49.0 3.37e-01 100.0% 88.4%
3589951 223.3.1.3 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Transpeptidase 0.55 49.0 3.28e-01 100.0% 91.2%
3806226 708.1.1.1 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › NAM 0.55 46.0 3.99e-01 95.9% 80.6%
3275455 4210.1.1.0 ↗ a+b two layers › WGR domain › WGR domain › WGR domain 0.53 45.0 4.25e-01 94.9% 79.2%
5068525 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.53 36.0 3.25e-01 70.4% 84.3%
4024578 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.52 38.0 3.29e-01 76.5% 65.8%
165196 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.52 38.0 3.56e-01 77.6% 79.7%
4681169 223.3.1.0 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins 0.52 46.0 3.08e-01 100.0% 70.5%
4670273 868.1.1.8 ↗ a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › SLS1_C 0.51 39.0 2.98e-01 82.7% 82.9%
4986643 2484.1.1.148 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_5 0.51 45.0 3.07e-01 100.0% 27.8%
2082805 243.3.1.1 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › Cystatin 0.51 34.0 3.58e-01 70.4% 80.4%
4999273 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.51 35.0 2.20e-01 73.5% 58.0%
4003463 220.1.1.168 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Tmpp129 0.50 41.0 3.87e-01 95.9% 71.2%
4985869 283.2.1.0 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like 0.50 36.0 3.82e-01 75.5% 98.9%
D3 high residues 1042-1115
PDB
D4 medium residues 11-21_92-114_211-329_414-453
PDB
Domain cluster: rep: replicase__YP_009179352__Aphis_glycines_virus_2_Viruses.__X__D99-112_203-276_293-321_386-433
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF22152.2 best Permu_RdRp_palm 183.2 9.40e-54 78.2% 37.2%
PF22152.2 Permu_RdRp_palm 51.1 1.30e-13 21.8% 11.5%
D5 medium residues 115-179
PDB
Domain cluster: representative
D6 medium residues 180-210_384-413
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2c0kB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.67 54.0 4.06e-01 88.5% 97.3%
1ashA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.64 49.0 3.80e-01 86.9% 100.0%
D7 medium residues 330-383_454-544
PDB
Domain cluster: rep: RdRp__YP_009337318__Hubei_permutotetra-like_virus_6__1923080__D328-384_485-539
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF22152.2 best Permu_RdRp_palm 96.9 1.60e-27 51.0% 20.4%
PF22152.2 Permu_RdRp_palm 57.2 1.80e-15 37.9% 14.8%
D8 medium residues 680-815
PDB
D9 medium residues 816-899
PDB