Back to structures

SR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00053

Bact-Vir

SR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00053

Identity

Kingdom:
phage

Quality

85.6 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 5-89
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r75102 3.30.1330.20 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Tubulin/FtsZ, C-terminal domain 0.67 48.0 4.42e-01 75.3% 58.2%
1ghhA00 3.30.910.10 Alpha Beta › 2-Layer Sandwich › Protein Binding, DinI Protein; Chain A › DinI-like 0.65 51.0 5.25e-01 98.8% 92.6%
4o89A02 3.30.360.20 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › RNA 3'-terminal phosphate cyclase, insert domain 0.64 50.0 4.92e-01 98.8% 77.7%
4euyA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.64 45.0 4.53e-01 90.6% 73.3%
2fa8B00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.63 46.0 4.57e-01 92.9% 73.6%
1w5eB02 3.30.1330.20 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Tubulin/FtsZ, C-terminal domain 0.63 46.0 4.25e-01 76.5% 66.0%
3pqvA02 3.30.360.20 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › RNA 3'-terminal phosphate cyclase, insert domain 0.63 52.0 5.06e-01 98.8% 81.2%
2os5A00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.61 51.0 4.60e-01 92.9% 74.6%
4b45A02 3.30.1330.20 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Tubulin/FtsZ, C-terminal domain 0.60 42.0 3.78e-01 76.5% 52.5%
3ec3A02 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.60 51.0 4.52e-01 92.9% 68.1%
4v1ag00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.59 44.0 3.71e-01 94.1% 45.9%
6nyyE01 1.20.58.760 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Peptidase M41 0.59 50.0 3.97e-01 91.8% 79.8%
2x49A01 3.40.30.60 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › FHIPEP family, domain 1 0.59 44.0 4.30e-01 100.0% 71.9%
2ig8A00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.58 38.0 3.21e-01 76.5% 40.1%
3cb2A02 3.30.1330.20 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Tubulin/FtsZ, C-terminal domain 0.57 39.0 3.74e-01 81.2% 60.6%
3rycB02 3.30.1330.20 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Tubulin/FtsZ, C-terminal domain 0.57 41.0 3.72e-01 80.0% 56.1%
2npbA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.57 42.0 4.23e-01 97.6% 78.4%
2es7A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.56 43.0 4.05e-01 97.6% 68.0%
1s3aA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 42.0 4.26e-01 92.9% 81.2%
1llnA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.55 45.0 3.61e-01 90.6% 86.3%
4f9zA02 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 46.0 4.18e-01 92.9% 68.1%
1t4yA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 45.0 4.50e-01 97.6% 87.6%
2diyA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 43.0 3.95e-01 92.9% 64.9%
2pptA02 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.54 43.0 4.03e-01 92.9% 68.9%
3apoA06 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.54 45.0 4.12e-01 92.9% 69.0%
2a4hA01 3.40.30.50 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Sep15/SelM thioredoxin-like domain, active-site redox motif 0.54 38.0 4.05e-01 94.1% 85.3%
2b5eA03 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 44.0 3.93e-01 92.9% 69.3%
4nwyA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 44.0 3.91e-01 94.1% 61.7%
3hz4A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 43.0 3.83e-01 94.1% 61.7%
7vw6B02 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 36.0 3.91e-01 91.8% 87.1%
1tvkA02 3.30.1330.20 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Tubulin/FtsZ, C-terminal domain 0.53 39.0 3.60e-01 80.0% 62.6%
4cw9B00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 40.0 3.82e-01 92.9% 69.2%
1sjiA03 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 43.0 3.88e-01 94.1% 69.4%
3gnjA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 41.0 3.80e-01 94.1% 65.8%
3tcoA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 42.0 3.90e-01 92.9% 69.8%
5j7dC00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 41.0 3.84e-01 92.9% 68.9%
6vu9A02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.52 44.0 3.20e-01 100.0% 33.9%
5aykA07 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 43.0 3.89e-01 90.6% 67.0%
3i3fB00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.51 40.0 3.50e-01 83.5% 100.0%
2r2jA03 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 42.0 3.68e-01 100.0% 57.6%
2nbsA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 39.0 3.58e-01 92.9% 62.1%
2dj0A01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 42.0 3.76e-01 92.9% 72.2%
1x5eA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 40.0 3.72e-01 94.1% 67.9%
2ycdA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 40.0 4.07e-01 92.9% 86.0%
2b5eA04 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 42.0 3.62e-01 97.6% 56.4%
3wgxB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.50 40.0 3.72e-01 92.9% 67.0%
2fy6A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.50 42.0 3.56e-01 92.9% 72.7%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4059350 315.2.1.1 a+b two layers › Tautomerase/MIF-like › DNA damage-inducible protein DinI › DNA damage-inducible protein DinI › DinI 0.71 57.0 6.06e-01 98.8% 98.7%
165987 301.6.1.2 a+b three layers › Bacillus chorismate mutase-like › Tubulin C-terminal domain-like › Tubulin C-terminal domain-like › FtsZ_C 0.67 48.0 4.16e-01 75.3% 49.2%
4964054 2485.1.1.34 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Rdx 0.66 46.0 4.90e-01 94.1% 82.7%
5033745 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.65 52.0 5.02e-01 98.8% 77.7%
4212654 315.2.1.1 a+b two layers › Tautomerase/MIF-like › DNA damage-inducible protein DinI › DNA damage-inducible protein DinI › DinI 0.65 54.0 5.59e-01 100.0% 98.8%
4937 315.2.1.1 a+b two layers › Tautomerase/MIF-like › DNA damage-inducible protein DinI › DNA damage-inducible protein DinI › DinI 0.65 51.0 5.25e-01 98.8% 92.6%
5041554 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.64 50.0 4.91e-01 98.8% 76.8%
312628 2485.1.1.34 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Rdx 0.64 46.0 4.61e-01 92.9% 74.4%
4888978 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.63 53.0 4.98e-01 98.8% 74.5%
5060057 2485.2.1.0 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain 0.63 54.0 5.03e-01 98.8% 76.2%
3599896 301.6.1.0 a+b three layers › Bacillus chorismate mutase-like › Tubulin C-terminal domain-like › Tubulin C-terminal domain-like 0.61 44.0 3.45e-01 76.5% 86.3%
3634941 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.60 45.0 4.35e-01 94.1% 70.5%
2644098 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.60 44.0 4.47e-01 97.6% 77.9%
3277433 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.60 45.0 4.09e-01 94.1% 59.1%
2718743 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.60 46.0 3.91e-01 95.3% 50.4%
5058032 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.60 41.0 3.12e-01 78.8% 32.4%
3195236 3016.1.1.0 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 0.59 51.0 5.10e-01 100.0% 92.2%
2883152 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.59 45.0 3.90e-01 94.1% 52.7%
3508676 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.59 44.0 4.09e-01 94.1% 63.8%
3516645 301.6.1.1 a+b three layers › Bacillus chorismate mutase-like › Tubulin C-terminal domain-like › Tubulin C-terminal domain-like › Tubulin_C 0.59 44.0 3.31e-01 80.0% 85.1%
3835475 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.59 45.0 4.00e-01 94.1% 57.5%
3476564 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.59 44.0 4.51e-01 96.5% 82.1%
3518732 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.59 44.0 3.83e-01 95.3% 51.1%
3989329 315.1.1.0 a+b two layers › Tautomerase/MIF-like › Tautomerase/MIF › Tautomerase/MIF 0.59 46.0 4.43e-01 83.5% 95.8%
5037375 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.59 40.0 3.58e-01 92.9% 50.0%
5057686 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.58 43.0 3.69e-01 90.6% 47.9%
3881647 2485.2.1.1 a+b three layers › Thioredoxin-like › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RNA 3'-terminal phosphate cyclase, RPTC, insert domain › RTC_insert 0.58 51.0 4.70e-01 98.8% 75.5%
2883302 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.58 44.0 3.53e-01 95.3% 40.6%
3479851 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.57 43.0 3.67e-01 94.1% 48.6%
4013321 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.57 43.0 4.16e-01 94.1% 72.3%
4027911 2485.1.1.90 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredox_PDIA6_C 0.57 48.0 4.26e-01 94.1% 64.8%
3605916 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.57 43.0 3.82e-01 95.3% 56.1%
3497363 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.56 43.0 3.93e-01 92.9% 62.7%
2791598 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.56 42.0 4.08e-01 95.3% 72.6%
3684591 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.56 40.0 4.01e-01 94.1% 75.3%
4676853 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.55 43.0 3.99e-01 98.8% 65.5%
3906157 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.55 42.0 3.99e-01 96.5% 69.0%
4954546 4038.1.1.0 alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein 0.55 47.0 3.36e-01 100.0% 72.1%
5064308 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.55 43.0 3.77e-01 83.5% 68.0%
3453594 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.55 41.0 4.01e-01 94.1% 72.6%
3088276 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.54 41.0 3.95e-01 95.3% 70.4%
3580076 2007.1.3.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like 0.54 38.0 3.31e-01 74.1% 54.6%
3218188 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.54 44.0 3.90e-01 89.4% 69.6%
3247200 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.54 46.0 4.18e-01 97.6% 70.4%
4486689 2485.1.1.78 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Suc_Fer-like 0.54 45.0 4.10e-01 97.6% 69.6%
5036541 301.6.1.0 a+b three layers › Bacillus chorismate mutase-like › Tubulin C-terminal domain-like › Tubulin C-terminal domain-like 0.53 37.0 3.24e-01 83.5% 46.9%
3479141 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.53 45.0 3.71e-01 92.9% 68.7%
3197853 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.53 39.0 4.17e-01 91.8% 90.7%
3594778 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.53 42.0 3.84e-01 89.4% 64.3%
3947685 4038.1.1.1 alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.52 45.0 3.41e-01 100.0% 84.0%
4028637 2485.1.1.1 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.52 42.0 3.90e-01 92.9% 68.2%
3493272 2485.1.1.1 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.52 42.0 3.87e-01 89.4% 67.3%
4943648 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.52 40.0 3.99e-01 94.1% 78.9%
3616979 2485.1.1.94 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › DJC16_C 0.52 45.0 3.69e-01 100.0% 61.8%
3975663 2485.1.1.26 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › HyaE 0.52 42.0 3.76e-01 94.1% 61.6%
3250262 2485.1.1.1 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.52 45.0 3.56e-01 98.8% 46.9%
4983100 301.6.1.2 a+b three layers › Bacillus chorismate mutase-like › Tubulin C-terminal domain-like › Tubulin C-terminal domain-like › FtsZ_C 0.52 35.0 3.26e-01 83.5% 53.0%
3492857 2485.1.1.19 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › L51_S25_CI-B8 0.51 43.0 3.71e-01 94.1% 57.9%
3942126 4038.1.1.8 alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Abc1-like 0.51 45.0 3.08e-01 100.0% 64.6%
4944139 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.51 42.0 3.59e-01 91.8% 64.3%
4975408 2485.1.1.1 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.51 40.0 3.64e-01 98.8% 63.5%
3424280 2485.1.1.1 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.50 40.0 3.81e-01 92.9% 74.0%
3223389 2485.1.1.1 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.50 41.0 3.84e-01 92.9% 70.9%