←Back to structures

readthrough_protein_-p99-

Euk-Vir

Japanese_iris_necrotic_ring_virus

readthrough_protein_-p99-__NP_038453__Japanese_iris_necrotic_ring_virus__77344

Identity

Accession:
NP_038453 ↗
Protein ID:
readthrough_protein_-p99-
Kingdom:
euk

Quality

73.5 mean pLDDT

Cluster

View cluster (58 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 608-755
PDB
Domain cluster: rep: P95_replicase__YP_009259667__Pelargonium_leaf_curl_virus__35280__D527-559_693-852
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 130.4 1.20e-37 90.5% 27.8%
D2 medium residues 79-189
PDB
Domain cluster: rep: replicase__YP_009037607__Moroccan_pepper_virus__208086__D159-283
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08500.17 best Tombus_P33 42.0 1.70e-10 90.1% 61.5%
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1e6vB02 1.20.840.10 Mainly Alpha › Up-down Bundle › Methyl-coenzyme M Reductase; Chain B, domain 2 › Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal 0.66 57.0 4.27e-01 95.5% 65.7%
1tt5B02 1.10.10.520 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 0.62 42.0 4.93e-01 82.9% 100.0%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.59 40.0 4.56e-01 97.3% 98.7%
1ls1A01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.58 38.0 4.16e-01 77.5% 80.9%
3b9qA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.57 36.0 3.94e-01 80.2% 77.5%
1ldjA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.57 45.0 4.54e-01 86.5% 94.8%
1t98A01 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 0.56 38.0 4.24e-01 85.6% 89.7%
3kl0A02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.56 42.0 3.12e-01 79.3% 38.9%
3fbzA01 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 40.0 4.17e-01 91.9% 84.3%
3cx5A02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.54 44.0 3.59e-01 91.9% 86.1%
2c0kB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 36.0 3.34e-01 71.2% 96.6%
1jm6B02 1.20.140.20 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain 0.53 39.0 3.51e-01 78.4% 93.0%
4ex8A00 3.40.1790.10 Alpha Beta › 3-Layer(aba) Sandwich › Indigoidine synthase fold › Indigoidine synthase domain 0.53 37.0 2.70e-01 73.0% 56.5%
1wgwA00 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.53 35.0 3.70e-01 80.2% 75.8%
7e5aB02 1.20.1000.10 Mainly Alpha › Up-down Bundle › Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 › Guanylate-binding protein, C-terminal domain 0.52 40.0 3.55e-01 82.0% 80.5%
2qsbA00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.52 33.0 3.72e-01 84.7% 84.7%
5jffA00 1.10.3290.10 Mainly Alpha › Orthogonal Bundle › Fic-like fold › Fido-like domain 0.51 41.0 3.51e-01 89.2% 58.0%
2fu2A00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.51 32.0 3.75e-01 82.9% 91.0%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3952621 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.75 46.0 5.64e-01 76.6% 98.6%
1211456 610.3.1.2 ↗ alpha arrays › ERP29 C domain-like › GatB/GatE C-terminal domain › GatB/GatE C-terminal domain › tRNA_synt_1c_R2,tRNA_synt_1c_R1 0.65 46.0 3.88e-01 74.8% 53.2%
3270407 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.62 52.0 3.77e-01 91.0% 37.5%
3817679 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.62 54.0 3.46e-01 95.5% 25.7%
3530124 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.62 36.0 4.17e-01 74.8% 80.0%
3170802 101.1.1.133 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Vhr1 0.61 46.0 4.93e-01 100.0% 93.7%
4014527 532.2.1.0 ↗ alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains 0.61 46.0 4.91e-01 81.1% 93.7%
3171699 101.1.1.133 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Vhr1 0.61 46.0 4.82e-01 100.0% 90.0%
3556488 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.60 52.0 3.36e-01 95.5% 26.2%
4609494 1197.1.1.1 ↗ alpha bundles › Integral membrane glycerol 3-phosphate acyltransferase PlsY › Integral membrane glycerol 3-phosphate acyltransferase PlsY › Integral membrane glycerol 3-phosphate acyltransferase PlsY › G3P_acyltransf 0.59 43.0 3.60e-01 76.6% 51.3%
3702110 593.1.1.0 ↗ alpha bundles › GroEL equatorial domain-like › GroEL equatorial domain-like › GroEL equatorial domain-like 0.57 46.0 3.56e-01 87.4% 100.0%
3699724 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.57 34.0 4.14e-01 91.9% 95.7%
3601089 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.56 35.0 3.97e-01 91.9% 86.3%
4934951 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.55 35.0 3.82e-01 81.1% 78.9%
3223469 168.1.1.1 ↗ alpha arrays › Sec7 domain › Sec7 domain › Sec7 domain › Sec7 0.54 47.0 3.88e-01 95.5% 55.4%
4026529 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.53 42.0 3.15e-01 86.5% 34.2%
4928737 592.2.1.0 ↗ alpha arrays › PWI domain-like › YugE-like › YugE-like 0.53 40.0 4.27e-01 86.5% 93.7%
4396592 7064.1.1.3 ↗ alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › FUSC_2 0.53 47.0 4.22e-01 96.4% 72.0%
3789554 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.53 40.0 4.31e-01 90.1% 97.8%
4028766 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.52 34.0 3.77e-01 78.4% 82.2%
4093848 3584.1.1.1 ↗ alpha arrays › DNA polymerase III finger domain › DNA polymerase III finger domain › DNA polymerase III finger domain › DNA_pol3_finger 0.52 44.0 3.56e-01 91.9% 58.1%
4962697 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.51 40.0 3.41e-01 83.8% 50.8%
5057661 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.51 32.0 3.62e-01 95.5% 83.5%
4974816 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.51 40.0 4.04e-01 84.7% 97.3%
4357455 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.51 35.0 3.88e-01 98.2% 92.9%
5005237 4967.1.1.11 ↗ alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › GIIM 0.50 36.0 3.25e-01 78.4% 51.9%
D3 medium residues 243-244_246-436_514-529
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337688__Beihai_tombus-like_virus_7__1922728__D528-588_642-697_774-796
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 210.7 5.40e-62 89.0% 35.8%
D4 medium residues 452-513_530-606
PDB
Domain cluster: rep: hypothetical_protein_1__YP_009337274__Changjiang_tombus-like_virus_14__1922807__D158-196_253-344
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00998.29 best RdRP_3 200.4 7.00e-59 100.0% 32.5%