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P3

Euk-Vir

Amphibola_crenata_associated_bacilladnavirus_1

P3__YP_009345104__Amphibola_crenata_associated_bacilladnavirus_1__1941435

Identity

Accession:
YP_009345104 ↗
Protein ID:
P3
Kingdom:
euk

Quality

59.9 mean pLDDT

Taxonomy

Shotokuvirae› Cressdnaviricota› Arfiviricetes› Baphyvirales› Bacilladnaviridae› Protobacilladnavirus› Amphibola_crenata_associated_bacilladnavirus_1

TaxID: 1941435

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 4-94
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vq8P03 1.10.1200.60 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.74 40.0 5.00e-01 89.0% 87.3%
3k7dA03 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.66 45.0 3.96e-01 70.3% 85.8%
3d1uA03 1.20.1270.240 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.63 45.0 4.35e-01 95.6% 66.3%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.63 48.0 4.79e-01 81.3% 93.8%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.63 44.0 4.63e-01 72.5% 90.4%
6vw7B03 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.62 44.0 4.54e-01 72.5% 91.7%
2xcqA02 3.90.199.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase II; domain 5 › Topoisomerase II, domain 5 0.62 44.0 3.17e-01 74.7% 84.1%
1jalA03 1.10.150.300 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain 0.61 41.0 4.34e-01 86.8% 77.8%
1jswA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.61 48.0 4.19e-01 84.6% 88.3%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.60 46.0 4.44e-01 81.3% 86.7%
2n7zA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.60 46.0 4.35e-01 89.0% 68.9%
3n98A01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.59 44.0 2.87e-01 78.0% 80.0%
7drjB01 1.20.120.1760 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain 0.59 44.0 3.51e-01 79.1% 54.1%
6ig5A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.58 53.0 4.55e-01 98.9% 89.9%
3mesA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.58 39.0 2.84e-01 70.3% 75.6%
4irlB02 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.57 41.0 4.14e-01 89.0% 73.1%
2nsfA01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.57 47.0 3.93e-01 91.2% 93.1%
1zp2A01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.57 41.0 3.77e-01 74.7% 78.3%
2yfqB01 1.10.8.1210 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.56 27.0 3.46e-01 75.8% 80.8%
3di5A00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.56 47.0 4.00e-01 93.4% 89.9%
2rd9B01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.55 45.0 3.66e-01 89.0% 82.9%
2hpsA00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.55 46.0 3.68e-01 93.4% 69.0%
1z19A01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.54 45.0 4.46e-01 95.6% 85.0%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.54 46.0 4.13e-01 94.5% 97.6%
1dcnA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.54 39.0 4.24e-01 81.3% 98.6%
5i41B00 1.10.1660.10 Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 › 0.53 32.0 3.67e-01 98.9% 82.1%
7e4gA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.53 46.0 3.68e-01 100.0% 78.2%
3i2fA02 1.10.3020.10 Mainly Alpha › Orthogonal Bundle › alpha-amino acid ester hydrolase ( Helical cap domain) › alpha-amino acid ester hydrolase ( Helical cap domain) 0.53 40.0 3.95e-01 80.2% 78.9%
2p1aB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.53 46.0 3.96e-01 96.7% 93.8%
1tj7A03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.53 38.0 4.20e-01 93.4% 100.0%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.53 40.0 4.26e-01 83.5% 97.5%
4asvA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.52 36.0 3.89e-01 94.5% 83.5%
1uaaA02 1.10.10.160 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.52 38.0 4.15e-01 78.0% 97.3%
1irxA05 1.10.10.350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.52 37.0 3.74e-01 74.7% 95.7%
1u8vB03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.52 43.0 3.28e-01 91.2% 69.5%
3cxbA03 1.10.1740.30 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › Secreted effector protein SifA helical domain 0.52 35.0 3.72e-01 95.6% 79.0%
4cpgA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.51 34.0 3.80e-01 92.3% 89.9%
3hr8A02 3.30.250.10 Alpha Beta › 2-Layer Sandwich › Rec A Protein; domain 2 › RecA protein, C-terminal domain 0.51 35.0 3.81e-01 89.0% 86.7%
6gy8A01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.51 41.0 2.85e-01 89.0% 79.8%
2ou6A00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.50 44.0 3.60e-01 100.0% 94.0%
2zj2A03 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 0.50 30.0 3.17e-01 72.5% 65.5%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3955218 632.2.1.17 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1707 0.75 38.0 5.25e-01 84.6% 100.0%
4020054 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.74 45.0 4.73e-01 87.9% 65.9%
3413217 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.71 40.0 3.65e-01 78.0% 44.3%
3271988 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.71 41.0 4.60e-01 94.5% 72.6%
3491875 4146.1.1.0 ↗ alpha bundles › YqgQ-like › YqgQ-like › YqgQ-like 0.69 45.0 5.52e-01 82.4% 100.0%
3952457 632.2.1.17 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1707 0.68 40.0 5.11e-01 83.5% 100.0%
4381440 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.67 38.0 3.49e-01 78.0% 44.3%
5036824 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.67 49.0 4.70e-01 76.9% 84.8%
4976222 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.66 49.0 4.58e-01 76.9% 80.0%
3781388 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.66 47.0 5.07e-01 75.8% 89.3%
4213337 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.66 48.0 4.71e-01 76.9% 87.0%
3628456 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.65 38.0 3.38e-01 78.0% 41.4%
4169057 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.65 48.0 4.74e-01 75.8% 91.6%
4561725 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.65 49.0 4.64e-01 78.0% 97.1%
5023598 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.65 49.0 4.72e-01 78.0% 98.0%
4114241 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.65 49.0 4.72e-01 78.0% 88.0%
4630813 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.64 50.0 4.65e-01 81.3% 97.3%
3771989 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.64 38.0 3.32e-01 75.8% 40.0%
3931606 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.64 38.0 3.51e-01 78.0% 47.0%
4178886 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.64 38.0 3.68e-01 75.8% 54.0%
5036014 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.64 35.0 3.52e-01 75.8% 52.6%
4984864 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.64 50.0 4.72e-01 83.5% 97.3%
3718200 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.63 39.0 3.49e-01 78.0% 45.6%
4938337 4952.1.1.1 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_1 0.63 52.0 4.71e-01 87.9% 95.8%
5029669 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.63 35.0 3.17e-01 78.0% 41.7%
3455582 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.62 54.0 5.05e-01 96.7% 76.4%
3996898 188.1.1.0 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain 0.62 50.0 3.91e-01 87.9% 54.9%
3365581 4952.1.1.1 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_1 0.61 48.0 4.47e-01 83.5% 93.0%
4933446 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.61 48.0 4.70e-01 90.1% 76.0%
4938609 4952.1.1.1 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_1 0.60 51.0 4.24e-01 91.2% 80.6%
4290275 4952.1.1.1 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_1 0.60 49.0 4.63e-01 86.8% 98.2%
5025553 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.60 48.0 4.68e-01 90.1% 77.0%
3810077 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.59 54.0 4.45e-01 97.8% 70.3%
3813741 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.59 54.0 4.60e-01 97.8% 79.3%
4457905 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.59 48.0 4.68e-01 90.1% 79.0%
3506967 632.1.1.11 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › HYOU1_C 0.59 41.0 4.13e-01 71.4% 94.4%
4988250 3745.1.1.1 ↗ alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex 0.58 40.0 2.81e-01 72.5% 73.1%
3607997 247.1.1.1 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B 0.57 46.0 3.07e-01 87.9% 82.0%
3710532 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.57 38.0 3.68e-01 78.0% 60.0%
4033 620.1.1.5 ↗ alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › MDMPI_N 0.57 47.0 3.93e-01 91.2% 92.5%
4999090 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.54 40.0 3.54e-01 75.8% 59.2%
5082966 2003.1.1.386 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Sacchrp_dh_C 0.54 44.0 2.85e-01 89.0% 79.8%
4029 620.1.1.0 ↗ alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases 0.54 46.0 4.02e-01 95.6% 95.8%
3520771 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.54 44.0 2.94e-01 90.1% 44.1%
5000181 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.53 38.0 3.61e-01 74.7% 61.8%
2721236 5001.1.1.6 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Bac_rhodopsin 0.53 46.0 3.67e-01 100.0% 77.4%
5070580 181.1.1.0 ↗ 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 0.53 34.0 4.03e-01 78.0% 98.3%
3597092 604.5.1.55 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PqiA 0.53 41.0 3.19e-01 85.7% 81.4%
4629841 150.3.1.16 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › IL15 0.52 36.0 3.22e-01 72.5% 58.5%
3651184 4957.1.1.7 ↗ a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit › MOM1 0.52 36.0 3.95e-01 72.5% 100.0%
4980050 620.1.1.0 ↗ alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases 0.51 45.0 3.90e-01 98.9% 87.9%
None — 0.50 37.0 2.87e-01 100.0% 32.7%
3392569 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.50 32.0 2.93e-01 75.8% 46.4%