←Back to structures

RdRp

Euk-Vir

Hubei_diptera_virus_13

RdRp__YP_009337911__Hubei_diptera_virus_13__1922874

Identity

Accession:
YP_009337911 ↗
Protein ID:
RdRp
Kingdom:
euk

Quality

95.6 mean pLDDT

Cluster

View cluster (85 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 1-29_206-223_295-313_357-438
PDB
Domain cluster: rep: RdRp__YP_009342464__Wuhan_house_centipede_virus_5__1923709__D21-63_232-262_353-368_387-474
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4rg9B01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.50 32.0 3.15e-01 84.5% 56.3%
D2 medium residues 30-48_81-121_145-177_272-294
PDB
Domain cluster: rep: NIa__YP_003620390__Freesia_mosaic_virus__421012__D109-224
D3 medium residues 49-80_224-256_314-356
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1cc8A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 39.0 4.62e-01 70.4% 90.3%
3mahA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.64 39.0 4.70e-01 70.4% 95.7%
1earA02 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.63 33.0 3.99e-01 70.4% 78.3%
3tj8A02 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.61 32.0 3.81e-01 70.4% 74.3%
1gmuA01 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.60 32.0 3.88e-01 70.4% 80.6%
3onqA02 3.30.70.2730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 38.0 4.31e-01 70.4% 88.9%
2j0wA04 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.57 38.0 4.40e-01 70.4% 97.3%
1konA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.56 32.0 3.71e-01 70.4% 80.0%
2p5vA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.56 36.0 4.03e-01 70.4% 85.7%
4oj3B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 35.0 3.72e-01 70.4% 73.7%
1vbkA01 3.30.70.1510 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › THUMP domain-like 0.54 36.0 4.05e-01 70.4% 90.4%
1yqhA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 35.0 3.62e-01 70.4% 69.2%
4mo0A00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.52 33.0 3.72e-01 70.4% 86.1%
2e29A01 3.30.70.2280 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 34.0 3.85e-01 70.4% 92.1%
1darA05 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 32.0 3.45e-01 70.4% 73.6%
3n89A02 3.30.310.210 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.52 35.0 3.29e-01 70.4% 54.7%
1vq8E02 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.51 35.0 3.71e-01 70.4% 96.8%
5i2cB01 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.50 35.0 3.16e-01 70.4% 57.5%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4946195 304.120.1.19 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › THUMP 0.68 39.0 4.80e-01 70.4% 93.8%
4990834 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.64 30.0 4.05e-01 70.4% 92.0%
5026555 304.120.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI 0.64 37.0 4.55e-01 70.4% 95.4%
4940504 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.64 33.0 4.25e-01 70.4% 90.0%
5293 304.22.1.1 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C 0.63 33.0 4.01e-01 70.4% 79.4%
4153537 304.22.1.1 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C 0.62 32.0 3.67e-01 70.4% 66.3%
3324584 304.24.1.6 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › SBDS_C 0.61 36.0 4.07e-01 70.4% 77.5%
4943447 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.61 36.0 4.25e-01 70.4% 85.3%
4946084 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.61 36.0 3.71e-01 70.4% 61.0%
3831150 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.60 36.0 3.96e-01 70.4% 74.1%
5026454 304.126.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C 0.60 34.0 4.07e-01 70.4% 89.2%
4501630 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.60 38.0 4.32e-01 70.4% 87.5%
5047509 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.59 35.0 3.63e-01 70.4% 61.0%
4427431 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.59 35.0 4.10e-01 70.4% 85.3%
4983501 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.59 39.0 4.46e-01 70.4% 91.3%
4948262 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.59 35.0 4.08e-01 70.4% 85.3%
4174001 304.22.1.1 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C 0.59 32.0 3.83e-01 70.4% 84.6%
4249416 304.22.1.1 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C 0.58 32.0 3.73e-01 70.4% 78.6%
4960543 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.58 31.0 3.94e-01 70.4% 91.7%
5039780 304.126.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C 0.58 34.0 4.19e-01 70.4% 96.9%
4107133 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.58 35.0 4.03e-01 70.4% 85.3%
4939665 304.120.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI 0.58 37.0 4.32e-01 70.4% 93.3%
4940609 304.8.1.21 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_9 0.58 38.0 4.23e-01 70.4% 84.7%
4118693 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.58 35.0 4.10e-01 70.4% 88.0%
5006888 304.22.1.2 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › PF26257 0.57 34.0 4.05e-01 70.4% 90.0%
4981261 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.57 32.0 3.75e-01 70.4% 78.7%
4127496 304.22.1.1 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C 0.57 31.0 3.61e-01 70.4% 74.7%
3603835 304.122.1.1 ↗ a+b two layers › Alpha-beta plaits › Nitrogen repressor-like proteins › Nitrogen repressor-like proteins › NRD1_2 0.56 34.0 3.45e-01 70.4% 60.0%
4099043 304.28.1.4 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › SecD_1st 0.56 37.0 4.24e-01 70.4% 96.0%
5026370 304.110.1.1 ↗ a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like › Acylphosphatase 0.56 37.0 3.83e-01 70.4% 72.7%
5023633 304.24.1.5 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N 0.56 32.0 3.82e-01 70.4% 87.1%
5078772 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.56 33.0 3.90e-01 70.4% 93.8%
3486643 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.55 38.0 3.78e-01 70.4% 95.5%
4374676 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.55 34.0 3.47e-01 70.4% 63.8%
3999364 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.54 35.0 3.62e-01 70.4% 69.4%
3626328 304.117.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.54 34.0 3.86e-01 70.4% 86.3%
4507904 304.120.1.6 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › ThiI_fer 0.54 36.0 4.15e-01 70.4% 98.7%
4555558 304.120.1.6 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › ThiI_fer 0.54 36.0 4.10e-01 70.4% 98.7%
3701334 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.53 31.0 3.32e-01 70.4% 65.3%
4064436 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.52 31.0 3.15e-01 70.4% 57.3%
4447636 304.28.1.4 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › SecD_1st 0.52 36.0 3.85e-01 70.4% 94.4%
4939726 212.1.1.17 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › EFG_IV 0.52 31.0 2.40e-01 70.4% 25.3%
5068324 304.24.1.5 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N 0.52 30.0 3.48e-01 70.4% 84.3%
4666097 212.1.1.0 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like 0.52 31.0 2.36e-01 70.4% 24.3%
1231422 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.52 31.0 3.12e-01 70.4% 57.4%
3339604 304.9.1.47 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › DUF4283 0.52 35.0 3.36e-01 70.4% 59.2%
4038458 101.1.2.28 ↗ alpha arrays › HTH › HTH › winged helix domain › eIF-5_eIF-2B 0.51 34.0 3.60e-01 96.3% 76.8%
4995344 101.1.2.28 ↗ alpha arrays › HTH › HTH › winged helix domain › eIF-5_eIF-2B 0.51 34.0 3.56e-01 96.3% 75.8%
4279487 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.51 30.0 3.05e-01 70.4% 59.0%
D4 medium residues 122-144_178-205_257-271
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1nv8B01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.60 27.0 2.63e-01 90.9% 38.0%
4cc9B00 1.20.5.4730 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.51 38.0 3.29e-01 77.3% 66.3%
2x6hA03 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.51 45.0 3.23e-01 100.0% 78.5%
1ki1B01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.51 39.0 2.88e-01 86.4% 87.4%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4993232 605.6.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › HP1531-like › HP1531-like 0.58 36.0 3.62e-01 98.5% 61.5%
3627578 109.4.1.532 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF4704 0.57 47.0 3.58e-01 95.5% 64.7%
3261051 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.50 38.0 3.98e-01 92.4% 86.7%
3584995 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.50 33.0 3.21e-01 100.0% 60.0%