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OP583594.1__WAX24197.1__P4_00039__00039

Bact-Vir

OP583594.1__WAX24197.1__P4_00039__00039

Identity

Accession:
OP583594 ↗
Kingdom:
phage

Quality

70.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Autographivirales› Autonotataviridae› Pradovirus› Xanthomonas_phage_P4

TaxID: 3003372

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 high residues 2-52
PDB
Domain cluster: representative
CATH (44)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6gdxA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.71 62.0 4.86e-01 100.0% 46.7%
4qclA02 3.30.70.2820 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 57.0 4.49e-01 100.0% 63.1%
4fvmA02 3.30.70.2820 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 56.0 4.57e-01 100.0% 55.3%
4rx6D00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 55.0 4.35e-01 100.0% 45.8%
4dkjA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.62 53.0 3.33e-01 100.0% 17.6%
7xlqD01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.62 45.0 3.41e-01 80.4% 83.7%
7o4xA01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 46.0 3.92e-01 100.0% 47.5%
4dpoB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 49.0 3.99e-01 100.0% 47.5%
1j2vA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 47.0 4.01e-01 100.0% 50.5%
2ek0A00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.59 47.0 4.13e-01 100.0% 62.2%
4f0qD01 2.30.280.20 Mainly Beta › Roll › PUA domain-like › 0.59 45.0 2.92e-01 84.3% 56.1%
1sqhA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.59 45.0 3.22e-01 100.0% 26.5%
3qv2A01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.59 49.0 3.32e-01 100.0% 24.5%
6fdfA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.58 46.0 3.26e-01 100.0% 25.6%
3e05B00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.58 50.0 3.39e-01 100.0% 27.6%
3d3sA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.58 47.0 3.44e-01 100.0% 31.4%
1p1lA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 45.0 3.88e-01 100.0% 50.0%
2yxdA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.57 50.0 3.42e-01 100.0% 29.1%
3bzwF00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.57 43.0 2.95e-01 92.2% 44.0%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 40.0 3.60e-01 82.4% 53.5%
1g5qA00 3.40.50.1950 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavin prenyltransferase-like 0.56 46.0 3.36e-01 100.0% 33.3%
1vq0A01 3.55.30.10 Alpha Beta › 3-Layer(bab) Sandwich › Hsp33 domain › Hsp33 domain 0.56 43.0 2.86e-01 88.2% 61.8%
3ewkA03 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 49.0 3.86e-01 100.0% 96.3%
3hm2A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 43.0 3.05e-01 88.2% 48.0%
1cx8A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.55 44.0 2.85e-01 98.0% 16.3%
1l3iA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 41.0 2.92e-01 86.3% 44.3%
2p35A01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 44.0 3.12e-01 100.0% 27.6%
2xzmJ00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.55 46.0 3.73e-01 100.0% 66.7%
6pfzD02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 42.0 2.72e-01 86.3% 46.3%
3g2eB00 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.55 41.0 2.83e-01 94.1% 22.7%
4bs9A03 3.30.1330.230 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › 0.54 45.0 3.36e-01 100.0% 51.7%
3lltA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.54 45.0 2.96e-01 98.0% 30.6%
4noiA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.54 44.0 3.67e-01 100.0% 52.4%
1ffyA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.54 44.0 2.68e-01 96.1% 41.4%
2n3gA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.54 42.0 3.77e-01 92.2% 61.1%
3icsA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 41.0 2.66e-01 86.3% 45.7%
3ttqA03 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 39.0 2.55e-01 80.4% 53.6%
6n2nA01 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.52 43.0 3.04e-01 100.0% 27.5%
4q8gA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.52 39.0 2.51e-01 90.2% 27.6%
5cvmA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 39.0 2.51e-01 90.2% 27.9%
3kd9A02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 39.0 2.55e-01 86.3% 45.8%
4cbgD02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 38.0 2.79e-01 84.3% 85.1%
6kghA02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.50 38.0 2.92e-01 94.1% 72.1%
6tmfM00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.50 40.0 3.39e-01 100.0% 69.6%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5046390 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.68 51.0 4.51e-01 100.0% 53.8%
5052024 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.66 54.0 4.73e-01 100.0% 60.0%
3603235 242.1.1.2 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2 0.64 51.0 4.19e-01 100.0% 46.0%
3309384 9.13.1.1 ↗ beta barrels › Lipocalins/Streptavidin › AOC barrel-like › AOC barrel-like › Dirigent 0.61 47.0 3.63e-01 86.3% 90.8%
3304622 2006.1.1.4 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › NIF 0.60 49.0 3.19e-01 100.0% 20.4%
3923319 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.59 40.0 2.64e-01 70.6% 71.9%
4932518 1036.1.1.1 ↗ a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.58 50.0 4.12e-01 100.0% 92.6%
3282895 912.1.1.0 ↗ few secondary structure elements › HIV-1 VPU cytoplasmic domain › HIV-1 VPU cytoplasmic domain › HIV-1 VPU cytoplasmic domain 0.57 43.0 2.98e-01 86.3% 23.6%
4989866 205.1.1.17 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4_11 0.56 38.0 2.52e-01 86.3% 16.4%
4797685 304.126.1.1 ↗ 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 › V_ATPase_I 0.56 44.0 3.60e-01 100.0% 43.4%
3271482 210.1.3.5 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_7 0.56 48.0 3.13e-01 100.0% 23.3%
5046705 328.1.1.0 ↗ a+b two layers › IF3-like › AlbA-like › AlbA-like 0.56 48.0 3.87e-01 100.0% 53.3%
3877917 223.1.1.98 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PF30670 0.56 48.0 3.57e-01 100.0% 70.0%
3489060 223.1.1.98 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PF30670 0.56 43.0 3.33e-01 84.3% 80.9%
3711494 4956.1.1.0 ↗ a+b two layers › ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.55 44.0 3.80e-01 100.0% 61.1%
5016531 11.1.1.347 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › T26-6p_Ig-like_dom_2 0.54 42.0 2.53e-01 86.3% 23.2%
5052927 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 37.0 2.88e-01 76.5% 87.4%
4629102 2484.1.1.36 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.53 40.0 2.39e-01 88.2% 35.0%
3912477 5001.1.1.5 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_3 0.53 36.0 2.32e-01 76.5% 13.1%
3235191 5001.1.1.41 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srw 0.53 42.0 2.64e-01 98.0% 29.3%
4159896 2003.1.1.59 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › NAD_binding_5 0.52 40.0 2.41e-01 86.3% 76.5%
3481564 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 40.0 3.51e-01 86.3% 61.3%
2726885 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 36.0 2.84e-01 74.5% 82.3%
4197190 812.1.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cell division protein MinE topological specificity domain › Cell division protein MinE topological specificity domain › MinE 0.52 41.0 4.00e-01 94.1% 88.3%
3455742 284.2.1.2 ↗ a+b two layers › FKBP-like › Chitinase insertion domain › Chitinase insertion domain › DUF8223 0.51 39.0 3.66e-01 84.3% 67.7%
3932435 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.51 39.0 2.43e-01 86.3% 87.8%
3612987 206.1.3.12 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › TTL 0.50 41.0 2.98e-01 94.1% 70.6%
5078578 304.51.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related 0.50 43.0 3.19e-01 100.0% 56.2%