Back to structures

SR-VP_0-2_scaffold_141_2510002_prodigal-single.1__X__X__00480

Bact-Vir

SR-VP_0-2_scaffold_141_2510002_prodigal-single.1__X__X__00480

Identity

Kingdom:
phage

Quality

75.0 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 9-71
PDB
Domain cluster: representative
CATH (59)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2i9cA01 1.25.40.70 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Phosphatidylinositol 3-kinase, accessory domain (PIK) 0.98 74.0 5.85e-01 82.5% 44.1%
2yxyA01 1.10.287.880 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Hypothetical protein YfhH domain 0.97 69.0 7.71e-01 73.0% 92.0%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.93 69.0 7.69e-01 77.8% 96.1%
1vh6A01 6.10.140.1940 Special › Helix non-globular › Helix Hairpins › 0.93 79.0 6.63e-01 88.9% 57.7%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.93 65.0 7.59e-01 73.0% 100.0%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.91 71.0 6.13e-01 82.5% 60.9%
3ro3A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.90 62.0 4.46e-01 76.2% 28.3%
4fymF00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.89 69.0 4.62e-01 81.0% 24.4%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.89 78.0 6.14e-01 95.2% 48.4%
3gw4A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.89 61.0 4.18e-01 76.2% 23.4%
3craB01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.88 73.0 6.46e-01 87.3% 69.8%
3gonA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.88 63.0 4.72e-01 73.0% 34.3%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.88 65.0 6.10e-01 79.4% 65.3%
2katA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.87 64.0 5.08e-01 81.0% 41.7%
1zs3A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.87 72.0 5.07e-01 87.3% 74.9%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.86 56.0 5.60e-01 73.0% 65.6%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.86 70.0 5.28e-01 85.7% 85.5%
3t9jA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.86 70.0 5.18e-01 85.7% 71.5%
2a9uA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.86 70.0 5.39e-01 85.7% 43.7%
3iq1B00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.85 69.0 5.00e-01 85.7% 79.2%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.85 66.0 5.86e-01 82.5% 64.4%
2fbnA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.85 64.0 4.70e-01 84.1% 32.7%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.85 65.0 4.55e-01 81.0% 27.4%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.85 63.0 5.86e-01 77.8% 64.5%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.84 65.0 5.94e-01 82.5% 68.3%
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 68.0 5.03e-01 85.7% 84.6%
2chpA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 68.0 5.05e-01 85.7% 85.8%
5tpmB00 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.84 59.0 4.43e-01 76.2% 32.6%
3unoE00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 67.0 4.82e-01 85.7% 32.9%
7e9uA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.84 70.0 4.09e-01 88.9% 29.9%
2gs4A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.83 73.0 5.34e-01 95.2% 87.3%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.83 70.0 5.93e-01 93.7% 56.9%
3lpzA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.83 61.0 3.77e-01 76.2% 15.9%
2pybA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.83 67.0 4.92e-01 85.7% 85.4%
3agtA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.82 65.0 5.06e-01 85.7% 40.6%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.82 61.0 5.89e-01 79.4% 94.4%
1s3qG00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.82 65.0 4.74e-01 85.7% 33.7%
2fjcB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.81 69.0 5.03e-01 90.5% 66.7%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.81 65.0 5.32e-01 87.3% 59.3%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.81 66.0 6.66e-01 90.5% 90.3%
1jgcA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.81 74.0 5.41e-01 100.0% 80.0%
1iipA02 1.10.150.160 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.80 67.0 6.11e-01 93.7% 71.8%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.80 68.0 5.98e-01 92.1% 78.9%
2vxxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.79 73.0 5.20e-01 100.0% 77.9%
3kwoA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.78 70.0 5.16e-01 95.2% 73.2%
3r2kA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.77 70.0 5.21e-01 100.0% 83.1%
2fcwA00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.77 63.0 5.38e-01 92.1% 68.9%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.77 64.0 6.12e-01 88.9% 88.7%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 65.0 6.30e-01 92.1% 85.5%
3n71A03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.76 66.0 4.57e-01 100.0% 29.1%
1rv2D04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.73 60.0 5.87e-01 95.2% 84.3%
1hr5A00 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 0.72 50.0 5.49e-01 74.6% 100.0%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.71 56.0 5.65e-01 85.7% 84.4%
2ke4A00 6.10.140.470 Special › Helix non-globular › Helix Hairpins › 0.69 57.0 5.04e-01 96.8% 92.9%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.68 55.0 4.14e-01 95.2% 35.4%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 54.0 5.31e-01 95.2% 84.5%
1wfdA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.66 54.0 4.87e-01 96.8% 76.3%
3fxdC00 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 0.65 47.0 5.09e-01 79.4% 100.0%
1vq8V00 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 48.0 4.85e-01 85.7% 96.9%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4432094 192.11.1.1 alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.97 68.0 7.84e-01 73.0% 95.8%
3240245 192.17.1.1 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › Rbsn 0.96 66.0 7.47e-01 71.4% 90.0%
None 0.96 73.0 4.16e-01 79.4% 9.7%
4228771 506.2.1.0 beta meanders › Colicin E3 ribonuclease domain-like › UvrB interaction domain › UvrB interaction domain 0.94 69.0 4.90e-01 76.2% 30.6%
3826508 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.94 66.0 6.57e-01 76.2% 70.8%
4324075 192.11.1.1 alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.94 69.0 7.81e-01 76.2% 100.0%
4582542 192.11.1.1 alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.93 65.0 6.50e-01 71.4% 76.2%
4530141 192.11.1.1 alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.93 70.0 7.80e-01 77.8% 98.0%
3707335 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.92 67.0 6.29e-01 76.2% 64.0%
4269685 192.11.1.1 alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.91 70.0 7.04e-01 79.4% 81.0%
4513708 192.11.1.1 alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.91 72.0 6.90e-01 82.5% 78.6%
4930198 605.1.1.2 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › H-kinase_dim 0.91 67.0 6.86e-01 76.2% 80.0%
4468502 192.11.1.1 alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.91 67.0 6.93e-01 77.8% 81.7%
4347101 5086.1.1.119 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › RRG1_C 0.90 76.0 6.61e-01 88.9% 62.2%
5025189 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.89 71.0 7.61e-01 84.1% 98.2%
3560750 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.89 72.0 6.91e-01 85.7% 77.1%
3336677 605.1.1.132 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › DUF641 0.88 70.0 6.57e-01 85.7% 70.7%
4930709 3877.1.1.0 alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.88 78.0 5.32e-01 95.2% 30.8%
5040777 6155.1.1.0 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.85 67.0 6.32e-01 84.1% 82.7%
3935050 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.85 60.0 3.86e-01 74.6% 18.4%
4127 159.1.2.2 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › MazG 0.84 65.0 5.91e-01 82.5% 67.5%
4477580 5086.1.1.118 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › BBS2_hp 0.84 74.0 6.62e-01 95.2% 69.4%
5008490 159.1.1.1 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › MazG 0.84 75.0 6.62e-01 96.8% 70.5%
4973840 4323.1.1.0 alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C 0.84 70.0 5.25e-01 92.1% 39.3%
4489484 2002.1.1.30 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.84 71.0 4.20e-01 90.5% 13.3%
3616031 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.84 69.0 5.92e-01 88.9% 57.9%
3738041 192.5.1.1 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.83 69.0 6.20e-01 90.5% 65.9%
3944931 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.81 72.0 6.30e-01 95.2% 96.7%
3560590 3755.3.1.142 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › FAM186A-B_C 0.81 68.0 5.15e-01 93.7% 40.0%
3186698 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.80 70.0 6.44e-01 95.2% 75.0%
3569669 4177.1.1.2 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.80 65.0 4.58e-01 90.5% 29.2%
4386662 3291.1.1.158 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Seryl_tRNA_N 0.80 69.0 5.52e-01 92.1% 51.3%
4514051 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.79 69.0 5.51e-01 92.1% 51.3%
3965106 605.1.1.4 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.79 65.0 6.17e-01 88.9% 76.0%
3389416 140.1.1.0 alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.77 55.0 4.67e-01 74.6% 48.0%
3473214 150.1.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.77 69.0 4.94e-01 100.0% 74.4%