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hypothetical_protein_pv_456

Euk-Vir

Pithovirus_sibericum

hypothetical_protein_pv_456__YP_009001357__Pithovirus_sibericum__1450746

Identity

Accession:
YP_009001357 ↗
Protein ID:
hypothetical_protein_pv_456
Kingdom:
euk

Quality

73.0 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Pithoviridae› Alphapithovirus› Pithovirus_sibericum

TaxID: 1450746

Cluster

Singleton — not in a non-trivial cluster

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 34-130
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5cwhA01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.65 48.0 4.15e-01 100.0% 49.4%
3ggyA00 1.20.1260.60 Mainly Alpha › Up-down Bundle › Ferritin › Vacuolar protein sorting-associated protein Ist1 0.61 45.0 3.68e-01 95.9% 40.9%
1z9eA00 1.20.930.10 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.61 48.0 5.09e-01 100.0% 100.0%
1upkA01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.57 48.0 3.47e-01 95.9% 41.9%
8a0rA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.57 51.0 4.66e-01 100.0% 80.8%
2odvA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 40.0 3.87e-01 74.2% 85.7%
2yv9B02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.56 50.0 4.51e-01 100.0% 91.0%
2d2sA01 1.20.58.1210 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, N-terminal helical domain 0.56 44.0 4.19e-01 100.0% 71.6%
2vq2A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.54 37.0 2.91e-01 100.0% 30.9%
2lt3A01 1.20.58.1290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › CarD-like, C-terminal domain 0.54 39.0 3.90e-01 93.8% 74.0%
1qqeA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 40.0 2.94e-01 100.0% 28.1%
2vvyA01 1.10.437.20 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › dsDNA poxvirus 0.52 40.0 3.69e-01 97.9% 61.2%
3k9iA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.51 40.0 3.95e-01 100.0% 78.6%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4003485 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 53.0 4.75e-01 92.8% 85.2%
3782168 109.4.1.1644 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec7-like_HDS, BIG2_C 0.59 52.0 3.26e-01 100.0% 23.3%
4976398 622.1.1.0 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain 0.59 53.0 5.25e-01 100.0% 94.2%
3172018 109.4.1.17 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cullin 0.58 48.0 4.89e-01 99.0% 92.6%
5062170 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 40.0 3.78e-01 79.4% 58.3%
3847200 109.4.1.563 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF3437 0.58 48.0 3.61e-01 93.8% 47.7%
3521246 109.4.1.1286 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_12 0.54 41.0 3.66e-01 99.0% 57.1%
3766260 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 46.0 3.48e-01 97.9% 47.8%
4391474 194.1.1.1 ↗ alpha complex topology › Serum albumin-like › Serum albumin-like › Serum albumin-like › Serum_albumin 0.53 37.0 2.93e-01 72.2% 35.2%
3827993 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 45.0 3.04e-01 100.0% 26.9%
D2 medium residues 131-221
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2cxhA01 3.40.50.10480 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Brix domain 0.63 39.0 3.16e-01 91.2% 32.8%
5tkwA01 3.30.420.380 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.62 51.0 4.20e-01 90.1% 97.1%
6em3x01 3.40.50.10480 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Brix domain 0.61 39.0 3.11e-01 93.4% 31.4%
4am6A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 48.0 3.75e-01 91.2% 95.2%
1t6cA02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.58 41.0 3.32e-01 74.7% 92.3%
4kruA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.56 47.0 3.64e-01 93.4% 93.5%
4hwtA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.56 34.0 3.23e-01 91.2% 48.2%
1qy9A02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.56 46.0 3.89e-01 92.3% 61.3%
1y9zA02 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.56 45.0 3.97e-01 91.2% 71.0%
3w4sA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.56 40.0 2.89e-01 75.8% 42.1%
2eo0B00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.55 44.0 4.07e-01 97.8% 66.1%
3n05A01 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.55 47.0 3.32e-01 95.6% 41.6%
1y0kA00 3.40.1540.10 Alpha Beta › 3-Layer(aba) Sandwich › Hypothetical protein pa4535 › Protein of unknown function DUF1780, putative endonuclease 0.55 46.0 3.80e-01 95.6% 81.0%
2ph7A02 3.40.50.10670 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › af2093 domain 0.54 42.0 4.20e-01 84.6% 88.5%
4ic1D00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.54 47.0 3.68e-01 98.9% 56.8%
1aj6A00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.54 42.0 3.34e-01 84.6% 49.5%
3mt0A00 3.40.50.12370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 43.0 3.11e-01 87.9% 31.7%
1vquB02 3.40.1030.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 › Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain 0.54 43.0 3.18e-01 90.1% 62.4%
2wteA01 3.40.50.11700 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 38.0 3.42e-01 76.9% 57.2%
3hj6A01 3.40.1190.30 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › 0.53 38.0 3.12e-01 76.9% 74.6%
1u9yA01 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 43.0 3.69e-01 89.0% 77.3%
6y04A01 3.40.1050.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-carbonic Anhydrase; Chain A › Carbonic anhydrase 0.52 43.0 3.56e-01 94.5% 89.3%
3qj4A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 37.0 3.18e-01 78.0% 49.7%
3js6A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 39.0 3.14e-01 84.6% 98.5%
3ewmA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 39.0 2.77e-01 83.5% 38.5%
1wn9A00 3.40.1530.10 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1805 › TTHA1528-like 0.51 39.0 3.59e-01 85.7% 98.4%
1ym5A01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.51 39.0 3.51e-01 84.6% 87.5%
1pjzA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 41.0 3.29e-01 92.3% 100.0%
1k28D04 3.30.1920.40 Alpha Beta › 2-Layer Sandwich › Phage tail proteins - 2 layer sandwich fold › 0.50 27.0 3.11e-01 74.7% 71.9%
3nojA01 3.50.30.40 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › Ribonuclease E inhibitor RraA/RraA-like 0.50 42.0 3.61e-01 94.5% 56.6%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3441795 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.64 52.0 3.46e-01 90.1% 99.0%
5069531 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.64 39.0 3.35e-01 91.2% 37.3%
4956492 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.62 39.0 3.18e-01 92.3% 33.1%
5057963 2492.1.1.1 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › dCMP_cyt_deam_1 0.62 51.0 4.44e-01 91.2% 93.8%
4024700 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.62 51.0 3.37e-01 92.3% 98.0%
4486867 3351.1.1.0 ↗ a/b three-layered sandwiches › Atg7 N-terminal domain-like › N-terminal domain in E1 enzyme Atg7 › N-terminal domain in E1 enzyme Atg7 0.61 45.0 4.42e-01 89.0% 72.0%
4023488 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.59 49.0 3.24e-01 93.4% 98.3%
3516319 7575.1.1.0 ↗ a/b three-layered sandwiches › Caspase-like › Caspase-like › Caspase-like 0.59 48.0 3.95e-01 91.2% 91.4%
3408206 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.58 49.0 4.18e-01 96.7% 66.9%
4309515 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.57 47.0 3.47e-01 90.1% 51.2%
4371923 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.57 45.0 3.37e-01 87.9% 50.4%
3649681 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.56 43.0 3.77e-01 82.4% 62.1%
5074452 2002.1.1.32 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Oxidored_FMN 0.55 48.0 3.36e-01 98.9% 79.4%
3272786 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.55 44.0 3.17e-01 90.1% 68.8%
3587896 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.55 43.0 3.04e-01 85.7% 81.3%
4666987 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.54 44.0 3.23e-01 89.0% 58.8%
3533544 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.54 44.0 3.07e-01 91.2% 70.1%
222168 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.54 47.0 3.68e-01 98.9% 56.8%
3250314 2007.2.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Flavoproteins 0.54 43.0 3.71e-01 86.8% 74.3%
5039697 2008.1.1.224 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_3 0.54 43.0 3.98e-01 90.1% 67.2%
3324891 207.1.1.79 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › F-box 0.54 43.0 3.04e-01 87.9% 43.3%
3446564 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.54 41.0 3.56e-01 82.4% 63.4%
4152182 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.54 41.0 4.14e-01 92.3% 82.1%
4390150 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.54 43.0 3.17e-01 90.1% 56.7%
3263345 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.54 44.0 3.08e-01 92.3% 64.4%
4971943 2008.1.1.77 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NOV_C 0.53 43.0 4.29e-01 95.6% 87.4%
5005296 2008.1.1.232 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF25941 0.53 45.0 4.17e-01 96.7% 74.2%
3429344 207.1.1.103 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_R13L1-DRL21 0.53 46.0 3.19e-01 98.9% 50.7%
374819 2487.1.1.8 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › RraA-like 0.53 42.0 3.30e-01 87.9% 80.1%
4981268 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.53 41.0 3.05e-01 85.7% 71.9%
3253990 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.53 42.0 2.86e-01 89.0% 63.1%
3277900 3105.1.1.3 ↗ a+b three layers › thylakoid acid phosphatase domain-related › thylakoid acid phosphatase domain-related › thylakoid acid phosphatase domain-related › DUF6676 0.53 37.0 3.45e-01 74.7% 98.3%
4986847 2008.5.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Uncharacterized protein AF_2093 C-terminal domain › Uncharacterized protein AF_2093 C-terminal domain › DUF6834_C 0.53 45.0 4.00e-01 97.8% 83.6%
4200176 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.53 42.0 2.85e-01 90.1% 64.3%
3427464 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.52 44.0 4.02e-01 95.6% 88.0%
4298034 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.52 42.0 3.19e-01 90.1% 60.4%
3249642 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.52 42.0 2.95e-01 93.4% 76.9%
3245311 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.52 36.0 3.48e-01 71.4% 98.1%
3822590 2008.1.1.77 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NOV_C 0.52 43.0 4.04e-01 96.7% 83.5%
4947849 2008.2.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.51 39.0 3.94e-01 91.2% 82.1%
4534000 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.51 41.0 3.24e-01 89.0% 61.0%
3940219 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.51 43.0 3.01e-01 96.7% 63.6%
4945204 2008.2.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.51 39.0 3.92e-01 91.2% 85.6%
5032325 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.50 41.0 3.36e-01 92.3% 94.1%
3201300 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.50 41.0 3.11e-01 90.1% 63.0%
5026996 2003.1.1.51 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › DFP 0.50 42.0 3.27e-01 95.6% 62.3%