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putative_5-3_exoribonuclease

Euk-Vir

Cafeteria_roenbergensis_virus_BV-PW1

putative_5-3_exoribonuclease__YP_003969670__Cafeteria_roenbergensis_virus_BV-PW1__693272

Identity

Accession:
YP_003969670 ↗
Protein ID:
putative_5-3_exoribonuclease
Kingdom:
euk

Quality

54.6 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Imitervirales› Mimiviridae› Rheavirus› Cafeteria_roenbergensis_virus_BV-PW1

TaxID: 693272

Cluster

View cluster (15 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 20-237
PDB
Domain cluster: rep: Hypothetical_protein_SPPV_50__NP_659626__Sheeppox_virus__10266__D1-82_143-236
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF03159.25 best XRN_N 74.7 1.10e-20 47.7% 40.2%
PF03159.25 XRN_N 44.2 2.20e-11 43.6% 34.0%
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2wteA01 3.40.50.11700 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.73 45.0 5.64e-01 95.4% 97.8%
4djaA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.71 43.0 4.92e-01 91.7% 79.8%
1xmxA01 3.40.50.10770 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Hypothetical protein VC1899 like domain (Restriction endonuclease-like) 0.69 43.0 5.22e-01 96.8% 93.7%
2kpoA00 3.40.50.11230 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.67 32.0 4.33e-01 94.5% 87.3%
3slrA02 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.62 43.0 4.97e-01 95.0% 96.2%
3rotA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.61 37.0 4.49e-01 78.4% 93.4%
3hcwA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.61 40.0 4.80e-01 78.4% 99.3%
1dbqA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.60 35.0 4.44e-01 96.3% 94.0%
2wjwA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.60 40.0 4.61e-01 89.4% 90.2%
3jvdA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.60 38.0 4.64e-01 76.6% 99.3%
2ah5A01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.60 39.0 4.69e-01 94.5% 98.6%
2no4B01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.59 40.0 4.64e-01 95.4% 96.7%
4zjpA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.59 39.0 4.66e-01 84.4% 100.0%
2qjoA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.59 41.0 4.38e-01 90.4% 79.6%
3brsA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 35.0 4.27e-01 95.9% 93.4%
3jy6D02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 36.0 4.44e-01 96.8% 99.3%
7s6eA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 35.0 4.33e-01 75.7% 97.0%
4rweA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 39.0 4.50e-01 84.9% 94.3%
3ctpA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 36.0 4.39e-01 76.6% 98.6%
5ce6A01 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.54 37.0 4.21e-01 95.4% 90.9%
1u04A03 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 39.0 4.25e-01 99.5% 89.3%
3i83A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 38.0 4.13e-01 96.3% 87.0%
1ab5A00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 31.0 3.93e-01 96.8% 96.8%
2amfA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 36.0 4.29e-01 95.9% 100.0%
3gt0A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 37.0 4.33e-01 96.8% 100.0%
2pv7A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 36.0 4.18e-01 99.1% 96.2%
2rcyA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 36.0 4.22e-01 98.2% 100.0%
7n29C01 3.40.50.10330 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Probable inorganic polyphosphate/atp-NAD kinase; domain 1 0.52 35.0 4.05e-01 97.7% 95.4%
1vffA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.52 42.0 3.41e-01 85.8% 82.7%
2x5nA01 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.51 40.0 4.41e-01 93.1% 100.0%
3egoA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 39.0 4.35e-01 96.3% 99.4%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3601601 2006.1.4.5 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.87 83.0 7.67e-01 98.6% 92.4%
4443696 2006.1.4.5 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.86 84.0 7.03e-01 100.0% 82.7%
3596146 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.86 74.0 7.72e-01 95.9% 95.1%
3716209 2006.1.4.5 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.85 80.0 6.58e-01 98.2% 69.1%
3251911 2006.1.4.5 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.84 75.0 7.51e-01 100.0% 90.9%
4027656 2006.1.4.5 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.84 80.0 7.68e-01 98.2% 92.1%
3595159 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.84 79.0 7.61e-01 97.2% 91.7%
3294273 2006.1.4.5 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.83 81.0 7.38e-01 100.0% 90.4%
3276794 2006.1.4.5 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.83 79.0 7.39e-01 98.2% 92.9%
3718959 2006.1.4.5 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.82 77.0 7.62e-01 97.2% 93.0%
3719108 2006.1.4.5 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.79 76.0 6.73e-01 100.0% 80.3%
2074443 2006.1.4.4 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.79 59.0 6.63e-01 97.2% 96.6%
4165496 2006.1.4.4 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.78 59.0 6.42e-01 96.3% 90.8%
4029535 2006.1.4.4 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.78 61.0 6.72e-01 96.8% 97.2%
5000538 2006.1.4.3 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › NYN 0.78 47.0 5.92e-01 96.3% 97.0%
3596632 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.78 74.0 7.06e-01 99.1% 92.8%
4943540 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.77 46.0 5.64e-01 96.3% 90.7%
3838776 2006.1.4.4 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.77 55.0 6.31e-01 96.3% 96.4%
4136793 2006.1.4.4 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.75 58.0 5.98e-01 96.3% 82.9%
3823952 2006.1.4.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.73 61.0 5.69e-01 99.5% 71.7%
4984967 7592.1.1.3 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › DUF6293_N 0.71 46.0 5.59e-01 95.4% 100.0%
3610118 2006.1.4.46 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N, XPG_I, XPG_I_2 0.71 60.0 5.48e-01 100.0% 68.3%
4024047 2006.1.4.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.70 63.0 6.20e-01 100.0% 89.1%
4426402 2006.1.4.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.69 58.0 5.87e-01 100.0% 87.7%
4984062 7592.1.1.3 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › DUF6293_N 0.69 47.0 5.56e-01 95.0% 98.7%
5072240 2006.1.4.25 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_I 0.69 57.0 5.96e-01 100.0% 94.5%
4938945 7592.1.1.3 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › DUF6293_N 0.68 45.0 5.46e-01 93.1% 100.0%
5010014 7592.1.1.0 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains 0.68 43.0 4.71e-01 95.4% 76.1%
3599611 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.68 60.0 5.48e-01 100.0% 71.9%
4931474 7592.1.1.3 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › DUF6293_N 0.66 47.0 5.42e-01 95.9% 97.5%
3594943 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.66 60.0 5.41e-01 100.0% 72.8%
3611555 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.66 59.0 5.33e-01 100.0% 71.7%
3521755 2006.1.4.3 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › NYN 0.66 45.0 5.15e-01 90.8% 93.8%
3818467 2006.1.4.3 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › NYN 0.64 46.0 5.29e-01 93.6% 100.0%
3989368 2003.1.1.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › F420_oxidored 0.63 40.0 4.65e-01 96.3% 87.7%
4972563 2006.1.1.43 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › HAD_PNKP 0.63 46.0 5.29e-01 93.1% 99.4%
5001495 2006.1.1.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.60 44.0 4.99e-01 92.2% 100.0%
4946471 2007.1.14.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like 0.58 34.0 4.28e-01 99.5% 97.6%
5035356 2006.1.4.3 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › NYN 0.57 49.0 5.13e-01 92.2% 98.0%
3476094 7590.1.1.2 ↗ a/b three-layered sandwiches › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Piwi 0.57 35.0 4.01e-01 98.6% 81.9%
5051848 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.56 53.0 4.62e-01 100.0% 73.1%
3744283 2003.1.1.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › F420_oxidored 0.56 39.0 4.25e-01 95.9% 87.4%
3594808 2006.1.1.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.55 47.0 4.64e-01 89.4% 89.5%
3587277 2010.1.1.3 ↗ a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › EIIA-man 0.55 33.0 4.20e-01 95.9% 100.0%
3266328 7514.1.1.3 ↗ a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › NAD_binding_6 0.55 44.0 4.80e-01 87.6% 100.0%
4972063 2006.1.1.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.54 48.0 4.84e-01 96.3% 93.8%
4026615 2007.1.16.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Iron-sulphur enzyme Dph2 › Diphthamide_syn 0.53 38.0 4.37e-01 92.2% 100.0%
4994385 2006.1.1.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.53 47.0 4.68e-01 96.3% 94.8%
3483447 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.53 38.0 4.35e-01 97.7% 98.8%
3786098 2004.1.1.65 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › 6PF2K 0.52 42.0 4.08e-01 83.5% 95.4%
169071 2003.1.1.30 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › ApbA 0.51 39.0 4.36e-01 95.9% 100.0%
5010523 2007.1.4.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Phosphofructokinase N-terminal domain › NAD_kinase 0.51 41.0 4.41e-01 96.3% 97.4%
D2 high residues 243-349
PDB
Domain cluster: rep: 5-3_exoribonuclease__YP_009001338__Pithovirus_sibericum__1450746__D237-336
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF17846.7 best XRN_M 32.8 5.50e-08 84.1% 16.3%
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.61 44.0 4.89e-01 86.9% 100.0%
3vayA02 1.20.120.1600 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.58 42.0 4.60e-01 79.4% 95.4%
2hi0A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.54 42.0 4.46e-01 83.2% 100.0%
2w02B01 1.10.150.640 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle 0.52 33.0 3.73e-01 87.9% 90.5%
7sf8A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.51 39.0 3.08e-01 83.2% 65.6%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4027649 3279.1.1.1 ↗ alpha arrays › Helical domain in 5'->3' exoribonucleases › Helical domain in 5'->3' exoribonucleases › Helical domain in 5'->3' exoribonucleases › XRN_M 0.75 69.0 5.00e-01 100.0% 53.2%
3595158 3279.1.1.0 ↗ alpha arrays › Helical domain in 5'->3' exoribonucleases › Helical domain in 5'->3' exoribonucleases › Helical domain in 5'->3' exoribonucleases 0.72 66.0 4.83e-01 100.0% 54.6%
3608857 3279.1.1.1 ↗ alpha arrays › Helical domain in 5'->3' exoribonucleases › Helical domain in 5'->3' exoribonucleases › Helical domain in 5'->3' exoribonucleases › XRN_M 0.72 66.0 4.78e-01 100.0% 55.9%
3999760 148.1.3.24 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_7 0.61 48.0 4.95e-01 98.1% 90.0%
5026918 148.1.3.17 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › MCM_lid 0.56 41.0 4.22e-01 76.6% 81.0%
3946728 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.55 45.0 4.67e-01 98.1% 100.0%
3458940 101.1.10.38 ↗ alpha arrays › HTH › HTH › Cyclin-like › DUF247 0.54 40.0 3.66e-01 77.6% 95.0%
D3 medium residues 357-473
PDB