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MK937597.1__QDH92317.1__SEA_SPOOKY_50__00050

Bact-Vir

MK937597.1__QDH92317.1__SEA_SPOOKY_50__00050

Identity

Accession:
MK937597 ↗
Kingdom:
phage

Quality

69.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Gordonia_phage_Spooky

TaxID: 2591210

Cluster

View cluster (2 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 medium residues 141-277_325-354
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2qywA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.81 39.0 5.25e-01 88.0% 84.2%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.73 42.0 5.34e-01 80.2% 94.9%
1h7cA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 40.0 5.14e-01 90.4% 100.0%
1s35A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 37.0 4.45e-01 88.6% 82.7%
1jmwA00 1.20.120.30 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartate receptor, ligand-binding domain 0.63 43.0 4.65e-01 70.1% 97.3%
6tkyA03 1.20.58.740 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DOCK DHR2 domain, lobe C 0.63 30.0 3.50e-01 85.6% 62.3%
1fewA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 43.0 4.27e-01 88.6% 67.6%
2odvA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 35.0 4.17e-01 88.6% 81.2%
4hteA01 1.20.58.1730 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 46.0 4.93e-01 88.6% 91.6%
1hciA03 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 34.0 3.95e-01 89.2% 80.8%
4mycA01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.54 44.0 3.48e-01 86.2% 43.6%
1dd5A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.53 30.0 3.68e-01 87.4% 86.2%
2cmrA00 1.20.58.1860 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 43.0 4.12e-01 87.4% 87.5%
1wteB01 1.10.3250.10 Mainly Alpha › Orthogonal Bundle › type ii restriction endonuclease, domain 1 › type ii restriction endonuclease, domain 1 0.51 30.0 3.24e-01 83.8% 66.0%
4mk3A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.51 34.0 4.05e-01 98.8% 98.3%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4564184 109.4.1.235 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SRP68 0.70 41.0 3.61e-01 85.0% 41.3%
3594486 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.70 46.0 5.39e-01 99.4% 91.7%
3923407 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.69 38.0 4.66e-01 88.6% 81.8%
3791250 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.67 47.0 4.91e-01 71.9% 92.3%
3254012 3684.1.1.0 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.65 46.0 4.59e-01 71.3% 97.1%
3580346 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.65 41.0 3.65e-01 89.2% 45.1%
3199608 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.63 38.0 4.56e-01 88.0% 90.0%
3936516 604.8.1.0 ↗ alpha bundles › Spectrin repeat-like › Smac/diablo › Smac/diablo 0.62 42.0 4.30e-01 89.2% 69.7%
3610601 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.61 43.0 3.86e-01 70.7% 94.7%
4507175 3285.1.1.1 ↗ alpha duplicates or obligate multimers › Alix V domain › Alix V domain › Alix V domain › ALIX_LYPXL_bnd 0.59 39.0 3.15e-01 80.2% 35.2%
3698113 604.1.1.132 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › KAR9 0.59 39.0 4.38e-01 85.0% 83.8%
3495636 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 55.0 3.69e-01 100.0% 31.5%
3624435 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 36.0 3.81e-01 88.6% 67.1%
3470779 3755.3.1.420 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › PTHB1_hp 0.57 47.0 4.26e-01 85.6% 94.4%
3695961 604.5.1.16 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › ArAE_2_N 0.54 47.0 3.84e-01 91.0% 91.5%
3598261 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.52 39.0 4.07e-01 89.8% 83.2%
3496367 603.2.1.0 ↗ alpha bundles › STAT-like › STAT › STAT 0.51 46.0 4.28e-01 100.0% 82.3%
D2 medium residues 355-418
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ydeB00 1.50.10.20 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.86 43.0 2.56e-01 73.4% 7.8%
4q5eA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.69 36.0 3.18e-01 79.7% 33.3%
1ykdB01 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.59 45.0 3.26e-01 82.8% 54.4%
1a2zA00 3.40.630.20 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Peptidase C15, pyroglutamyl peptidase I-like 0.59 46.0 3.13e-01 82.8% 95.5%
1sfxB00 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 0.57 46.0 3.94e-01 87.5% 90.4%
2kz6A01 6.10.140.1310 Special › Helix non-globular › Helix Hairpins › 0.56 45.0 4.25e-01 100.0% 72.8%
5jnbA01 1.10.1410.10 Mainly Alpha › Orthogonal Bundle › Poly(a)-polymerase, middle domain › 0.55 38.0 2.70e-01 73.4% 32.3%
2anvA00 1.10.530.40 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.53 41.0 3.25e-01 87.5% 44.5%
4hjhA03 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.53 38.0 3.17e-01 76.6% 89.6%
2mraA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.53 43.0 3.46e-01 85.9% 97.4%
1hqmD05 3.90.105.10 Alpha Beta › Alpha-Beta Complex › Molybdopterin biosynthesis moea protein, domain 2 › Molybdopterin biosynthesis moea protein, domain 2 0.52 36.0 3.48e-01 73.4% 64.0%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4244236 3681.1.1.0 ↗ a+b complex topology › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit 0.76 56.0 4.61e-01 78.1% 76.4%
3385861 3747.1.1.2 ↗ a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flg_bb_rod,Flg_bbr_C 0.69 60.0 4.65e-01 92.2% 77.5%
3071039 244.1.1.9 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › GMC_oxred_C 0.65 45.0 3.03e-01 71.9% 78.3%
2724318 3747.1.1.2 ↗ a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flg_bb_rod,Flg_bbr_C 0.64 58.0 4.56e-01 100.0% 83.8%
5042455 101.1.2.92 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_11 0.64 57.0 4.57e-01 96.9% 84.0%
4939519 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.63 56.0 4.64e-01 96.9% 91.8%
4931729 101.1.2.953 ↗ alpha arrays › HTH › HTH › winged helix domain › PF29890 0.62 49.0 3.91e-01 85.9% 88.0%
4946669 4045.1.1.1 ↗ a+b two layers › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › Aminotran_4 0.61 42.0 3.00e-01 71.9% 96.3%
4978893 3755.3.1.632 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › Prefoldin 0.60 56.0 4.23e-01 100.0% 47.9%
4020933 1075.1.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane 0.58 48.0 3.11e-01 90.6% 54.8%
5037761 7528.1.1.0 ↗ a/b three-layered sandwiches › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains 0.54 42.0 3.15e-01 87.5% 84.6%
159686 235.1.1.6 ↗ a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Phage_lysozyme 0.53 41.0 3.25e-01 87.5% 44.5%
3949298 235.1.1.6 ↗ a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Phage_lysozyme 0.53 46.0 3.35e-01 96.9% 57.1%
4202672 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.52 45.0 3.00e-01 93.8% 46.0%
2771202 235.1.1.6 ↗ a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Phage_lysozyme 0.52 42.0 3.21e-01 92.2% 41.2%
3597631 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 43.0 2.88e-01 93.8% 49.8%
4039729 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.50 34.0 3.01e-01 71.9% 46.0%