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OQ756160.1__WHM53144.1__XAP3_0047__00047

Bact-Vir

OQ756160.1__WHM53144.1__XAP3_0047__00047

Identity

Accession:
OQ756160 ↗
Kingdom:
phage

Quality

92.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Casjensviridae› Zhonglingvirus› Xanthomonas_phage_XAP3

TaxID: 3043621

Cluster

View cluster (6 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 high residues 9-80
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1wczA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.65 45.0 3.89e-01 83.3% 46.1%
7cfdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.62 42.0 4.26e-01 97.2% 69.9%
4lduA03 2.30.30.1040 Mainly Beta › Roll › SH3 type barrels. › 0.62 46.0 4.74e-01 79.2% 92.6%
4qqgG00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.60 44.0 4.46e-01 80.6% 79.2%
2vb6A01 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.59 41.0 4.59e-01 95.8% 96.3%
4g1vA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.58 44.0 3.72e-01 80.6% 60.2%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 44.0 3.21e-01 84.7% 39.7%
2rovA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 42.0 3.72e-01 84.7% 86.3%
4h75A00 2.80.10.70 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › Spindlin/Ssty 0.56 42.0 3.08e-01 80.6% 29.1%
6r3wA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 45.0 3.59e-01 95.8% 95.0%
3r5lA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 42.0 3.60e-01 83.3% 53.4%
2avwD01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.55 40.0 3.31e-01 80.6% 92.9%
2o62A02 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 44.0 3.76e-01 95.8% 91.2%
3ebwA01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 44.0 3.73e-01 100.0% 97.2%
2ptfA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 43.0 3.50e-01 91.7% 56.5%
3bbaA00 3.90.70.50 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Streptopain (SpeB) 0.52 38.0 2.73e-01 80.6% 26.4%
6mv2A02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.52 38.0 3.39e-01 77.8% 69.5%
2f5tX02 2.30.30.690 Mainly Beta › Roll › SH3 type barrels. › 0.51 38.0 3.58e-01 80.6% 70.0%
2ebfX01 3.10.670.10 Alpha Beta › Roll › Secreted effector protein ssei fold › Secreted effector protein ssei. 0.51 40.0 3.02e-01 88.9% 47.7%
3njaA02 2.10.70.100 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.51 28.0 3.42e-01 100.0% 87.0%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3564421 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 47.0 4.09e-01 80.6% 79.1%
4968263 1.1.5.91 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_C 0.63 53.0 3.74e-01 93.1% 46.8%
4945477 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.60 48.0 3.18e-01 87.5% 36.8%
3315951 220.1.1.86 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › ZGRF1-like_N 0.60 44.0 4.35e-01 80.6% 91.1%
3520654 4.1.1.187 ↗ beta barrels › SH3 › SH3 › SH3 › DIRP 0.60 40.0 3.20e-01 80.6% 34.0%
3182025 4.1.1.475 ↗ beta barrels › SH3 › SH3 › SH3 › PF26640 0.59 44.0 3.58e-01 80.6% 48.1%
3928136 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 41.0 4.46e-01 79.2% 88.3%
55 1.1.5.31 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyridox_ox_2 0.57 44.0 3.26e-01 84.7% 41.8%
3632407 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 43.0 3.76e-01 84.7% 78.6%
3633294 219.1.1.93 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › DUF6540 0.55 45.0 3.74e-01 94.4% 97.1%
5024617 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.54 40.0 3.70e-01 80.6% 64.2%
3907134 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.53 41.0 2.99e-01 86.1% 28.6%
3719783 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.53 40.0 3.66e-01 80.6% 76.6%
3636807 1.1.5.30 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyridox_oxase_2 0.53 47.0 3.15e-01 100.0% 63.2%
3924619 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 42.0 3.60e-01 100.0% 54.2%
5041801 4.15.1.0 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like 0.52 37.0 3.58e-01 80.6% 64.7%
5026284 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.52 39.0 3.58e-01 80.6% 64.2%
5025498 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.52 37.0 3.54e-01 79.2% 64.4%
4024274 4.1.1.17 ↗ beta barrels › SH3 › SH3 › SH3 › Ribosomal_L19 0.52 38.0 3.43e-01 80.6% 61.0%
5037370 4200.1.1.0 ↗ beta barrels › YmcC-like › YmcC-like › YmcC-like 0.51 37.0 3.04e-01 79.2% 94.4%
3974873 219.1.1.35 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › SpvD 0.51 37.0 2.77e-01 80.6% 31.4%
3611370 209.1.1.0 ↗ a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like 0.51 38.0 2.80e-01 81.9% 57.5%
3436557 220.4.1.8 ↗ beta barrels › PH domain-like › second barrel domain in viral glycoproteins › second barrel domain in viral glycoproteins › ZGRF1-like_N 0.50 36.0 3.62e-01 80.6% 98.7%
D2 high residues 81-143
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1bhaA00 1.10.287.170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.84 45.0 4.40e-01 79.4% 49.3%
7csoA01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.80 54.0 3.62e-01 82.5% 20.0%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.75 50.0 5.32e-01 84.1% 77.2%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.75 48.0 4.87e-01 82.5% 67.2%
7zxkC01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.74 47.0 3.46e-01 79.4% 26.7%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 47.0 4.52e-01 79.4% 59.2%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 45.0 4.64e-01 77.8% 69.0%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 51.0 5.12e-01 79.4% 74.6%
2jqqA00 1.20.58.1240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 49.0 3.61e-01 77.8% 29.9%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.69 46.0 4.70e-01 76.2% 71.7%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.69 39.0 3.50e-01 73.0% 41.2%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.68 50.0 4.92e-01 77.8% 71.6%
6cgaC02 1.20.58.860 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 49.0 4.53e-01 76.2% 65.4%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.67 46.0 4.10e-01 77.8% 51.1%
2oyyA00 6.10.80.10 Special › Helix non-globular › DNA polymerase; domain 1 › Hexameric tyrosine-coordinated heme protein (HTHP) 0.67 49.0 4.80e-01 81.0% 74.6%
2ozbB01 1.10.287.4070 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.66 48.0 3.75e-01 76.2% 74.0%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.66 43.0 4.47e-01 73.0% 71.2%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.64 44.0 4.35e-01 73.0% 68.2%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 46.0 4.24e-01 79.4% 59.3%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 42.0 3.43e-01 76.2% 36.8%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.61 40.0 4.19e-01 73.0% 74.1%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.61 43.0 4.37e-01 74.6% 79.7%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.61 44.0 3.75e-01 77.8% 47.2%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 44.0 3.54e-01 77.8% 41.7%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 48.0 4.48e-01 88.9% 93.4%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 42.0 3.92e-01 76.2% 62.8%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.58 45.0 4.03e-01 82.5% 67.1%
1h97A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.55 46.0 3.57e-01 95.2% 42.9%
3iylB02 1.10.2050.10 Mainly Alpha › Orthogonal Bundle › Protein mu-1, chain B, domain 3 › Protein mu-1, chain B, domain 3 0.53 42.0 3.45e-01 92.1% 76.9%
2whnA00 1.20.81.30 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › Type II secretion system (T2SS), domain F 0.52 44.0 3.66e-01 92.1% 72.7%
4ip8A00 1.10.132.110 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Serum amyloid A protein 0.51 40.0 3.27e-01 81.0% 57.1%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3783731 2004.1.1.505 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, AAA_30 0.80 50.0 2.96e-01 79.4% 9.5%
4638470 101.1.2.311 ↗ alpha arrays › HTH › HTH › winged helix domain › RNA12 0.80 59.0 4.20e-01 77.8% 62.4%
4396464 605.1.1.305 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Exonuc_VII_S 0.78 49.0 5.02e-01 79.4% 66.7%
5060491 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.78 51.0 4.02e-01 77.8% 35.0%
3322575 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.77 47.0 2.97e-01 88.9% 14.4%
3684835 3712.1.1.1 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Med11 0.76 52.0 4.45e-01 90.5% 47.4%
3284776 5010.1.1.0 ↗ extended segments › Bacterial aa3 type cytochrome c oxidase subunit IV › Bacterial aa3 type cytochrome c oxidase subunit IV › Bacterial aa3 type cytochrome c oxidase subunit IV 0.73 43.0 4.62e-01 88.9% 69.1%
3291034 3271.1.1.1 ↗ alpha arrays › CdiA C-terminal nuclease domain › CdiA C-terminal nuclease domain › CdiA C-terminal nuclease domain › Ntox28 0.72 45.0 3.88e-01 79.4% 42.1%
3623760 604.1.1.3 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › MAP65_ASE1 0.71 51.0 4.16e-01 76.2% 82.6%
3587894 101.1.2.49 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR,Vir_act_alpha_C 0.70 50.0 3.59e-01 76.2% 26.9%
4848962 3016.1.1.5 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SHMT 0.68 42.0 3.92e-01 82.5% 48.8%
3813837 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.67 45.0 4.31e-01 81.0% 58.7%
3962961 150.5.1.53 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › PPE 0.66 46.0 4.25e-01 77.8% 57.5%
3542037 109.4.1.1428 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_Edg1 0.59 41.0 2.76e-01 73.0% 22.9%
3623198 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.57 39.0 3.69e-01 74.6% 57.5%
3736652 192.29.1.102 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Fung_rhodopsin 0.55 39.0 3.62e-01 77.8% 58.7%
3453972 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.54 46.0 3.41e-01 88.9% 40.7%