←Back to structures

NC_060133.1__YP_010246117.1__L3Y21_gp004__00004

Bact-Vir

NC_060133.1__YP_010246117.1__L3Y21_gp004__00004

Identity

Accession:
NC_060133 ↗
Kingdom:
phage

Quality

86.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Nevillevirus› Gordonia_phage_Rabbitrun

TaxID: 2762280

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 medium residues 1-40
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
8eb0A01 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.82 66.0 5.05e-01 92.5% 40.7%
2gviA03 3.30.60.20 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.76 58.0 6.18e-01 90.0% 97.1%
1zbdB00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.75 67.0 4.68e-01 100.0% 34.1%
3goxA02 3.30.60.130 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.75 65.0 5.94e-01 100.0% 83.3%
1wimA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.73 62.0 4.73e-01 100.0% 41.5%
1wfkA01 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.73 65.0 5.20e-01 100.0% 62.3%
3t7lA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.72 64.0 5.18e-01 100.0% 59.5%
2xzm500 3.30.1740.20 Alpha Beta › 2-Layer Sandwich › first zn-finger domain of poly(adp-ribose) polymerase-1 › Ribosomal protein S26 0.68 56.0 4.22e-01 95.0% 68.4%
2d8yA01 2.10.110.10 Mainly Beta › Ribbon › Cysteine Rich Protein › Cysteine Rich Protein 0.66 55.0 4.61e-01 97.5% 66.7%
5tabA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.64 49.0 4.49e-01 85.0% 66.0%
3o70A00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.63 54.0 4.89e-01 97.5% 69.1%
4qf3A00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.63 53.0 4.77e-01 95.0% 73.7%
2ecjA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.63 48.0 4.42e-01 100.0% 62.1%
5fb0C01 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.62 50.0 4.55e-01 100.0% 67.2%
1vx7000 2.30.170.20 Mainly Beta › Roll › Ribosomal Protein L24e; Chain: T; › Ribosomal protein L24 0.62 52.0 4.60e-01 100.0% 67.7%
2vp7A00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.60 47.0 4.07e-01 90.0% 56.1%
4e1pA00 3.30.60.230 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › Lsr2, dimerisation domain 0.60 51.0 4.64e-01 100.0% 76.4%
2xb1A00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.58 51.0 3.88e-01 100.0% 51.0%
2xjyA01 2.10.110.10 Mainly Beta › Ribbon › Cysteine Rich Protein › Cysteine Rich Protein 0.58 47.0 4.13e-01 97.5% 60.3%
5b3hC01 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.56 36.0 3.47e-01 87.5% 54.2%
2g43B01 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.51 38.0 2.97e-01 87.5% 37.8%
ECOD (67)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3397474 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.82 72.0 7.26e-01 97.5% 97.5%
3798139 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.82 75.0 5.43e-01 100.0% 41.1%
3573660 376.1.1.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4 0.80 67.0 5.20e-01 97.5% 43.5%
3627614 376.1.3.3 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › FYVE 0.80 68.0 5.77e-01 92.5% 60.0%
4929415 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.80 69.0 5.98e-01 100.0% 63.3%
3910122 376.1.3.4 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › FYVE_2 0.80 68.0 5.63e-01 100.0% 54.3%
5021070 377.1.1.5 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › LIM 0.80 63.0 6.61e-01 95.0% 100.0%
4940040 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.78 63.0 6.11e-01 97.5% 80.0%
3643916 375.1.1.235 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › ADD_ATRX 0.78 68.0 6.83e-01 100.0% 97.5%
3720327 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.78 69.0 5.01e-01 100.0% 39.0%
3636589 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.77 65.0 4.97e-01 100.0% 42.2%
4024032 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.77 64.0 4.97e-01 97.5% 43.5%
3561303 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.77 67.0 4.41e-01 100.0% 24.2%
4979944 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.77 65.0 6.51e-01 95.0% 100.0%
8199 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.76 58.0 6.24e-01 90.0% 100.0%
3636674 376.1.1.3 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › ZZ 0.76 67.0 6.24e-01 95.0% 77.6%
3468455 376.1.3.16 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › ADD_ATRX 0.75 65.0 6.54e-01 100.0% 97.5%
3849360 376.1.3.23 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › RIM2a_ZnF 0.75 67.0 5.39e-01 100.0% 64.0%
3881136 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.75 66.0 6.16e-01 100.0% 82.0%
3718357 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.75 56.0 5.44e-01 87.5% 73.3%
5008357 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.74 56.0 5.94e-01 90.0% 94.3%
4998890 377.1.1.7 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › zf-dskA_traR 0.74 57.0 5.46e-01 90.0% 73.3%
4957868 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.74 56.0 5.87e-01 95.0% 94.3%
3634446 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.73 57.0 5.52e-01 92.5% 75.6%
5053624 377.1.1.7 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › zf-dskA_traR 0.73 51.0 5.63e-01 82.5% 100.0%
3962784 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.73 59.0 6.19e-01 90.0% 100.0%
3608274 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.73 64.0 5.78e-01 100.0% 72.7%
5041606 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.73 65.0 5.50e-01 100.0% 63.1%
3728775 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.72 62.0 4.83e-01 97.5% 45.9%
3395505 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.71 54.0 5.30e-01 92.5% 77.8%
1779555 377.1.1.22 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › Stc1 0.71 59.0 5.89e-01 100.0% 95.1%
3594353 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.71 55.0 4.72e-01 87.5% 53.8%
3671431 376.1.1.40 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_11 0.70 57.0 5.57e-01 97.5% 82.2%
4466003 376.1.3.44 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › Siva 0.70 58.0 4.99e-01 95.0% 63.1%
3372361 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.69 57.0 5.71e-01 95.0% 100.0%
3566304 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.69 57.0 5.77e-01 92.5% 95.0%
3410688 376.1.3.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD 0.68 59.0 5.45e-01 95.0% 76.0%
4442858 931.1.1.15 ↗ few secondary structure elements › Metallothionein › Metallothionein › Metallothionein › PF26927 0.68 53.0 5.49e-01 92.5% 100.0%
3912396 376.1.3.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD 0.68 60.0 5.43e-01 100.0% 74.5%
3398201 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.68 59.0 4.55e-01 100.0% 71.1%
3489435 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.67 57.0 4.83e-01 100.0% 61.4%
3499889 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.67 52.0 5.46e-01 92.5% 100.0%
3646133 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.67 54.0 5.30e-01 95.0% 86.7%
4945028 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.66 56.0 4.67e-01 100.0% 54.1%
3297615 376.1.3.25 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD-1st_NSD 0.66 58.0 5.24e-01 100.0% 72.7%
3846283 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.66 57.0 5.33e-01 100.0% 82.0%
3256364 377.1.1.5 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › LIM 0.66 54.0 4.66e-01 100.0% 68.6%
3660754 376.1.3.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD 0.64 52.0 3.88e-01 92.5% 37.1%
3722098 376.1.1.61 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › Rtf2 0.64 54.0 4.65e-01 97.5% 60.0%
3301385 376.1.3.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD 0.63 51.0 3.84e-01 92.5% 39.0%
3323549 376.1.1.20 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_UBOX 0.63 54.0 4.93e-01 100.0% 72.7%
5081423 378.1.1.3 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › Endonuclease_7 0.62 52.0 4.29e-01 95.0% 52.7%
4000791 377.1.1.5 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › LIM 0.62 48.0 4.87e-01 95.0% 90.0%
3183646 376.1.1.61 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › Rtf2 0.62 50.0 4.10e-01 97.5% 47.0%
4946420 376.1.1.180 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › ResIII 0.61 50.0 4.36e-01 97.5% 60.0%
3216239 376.1.3.9 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD_2 0.60 48.0 4.15e-01 95.0% 68.6%
3184687 376.1.6.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › IBR domain 0.60 42.0 4.28e-01 82.5% 95.0%
3268166 376.1.3.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD 0.60 46.0 4.42e-01 97.5% 72.0%
4670436 375.1.1.284 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › PF27208 0.57 46.0 4.69e-01 100.0% 100.0%
4430351 376.1.3.4 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › FYVE_2 0.57 45.0 4.08e-01 87.5% 81.8%
5007944 377.1.1.126 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › Arc_trans_TRASH 0.56 46.0 4.67e-01 100.0% 100.0%
4928198 2002.3.1.2 ↗ a/b barrels › TIM beta/alpha-barrel › Glycoside hydrolase/deacetylase › Glycoside hydrolase/deacetylase › Polysacc_deac_1 0.56 39.0 2.55e-01 80.0% 85.2%
3394481 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.55 43.0 4.40e-01 97.5% 92.5%
4625359 7101.1.1.1 ↗ extended segments › Prp8-binding region of SLU7 › Prp8-binding region of SLU7 › Prp8-binding region of SLU7 › Slu7 0.53 30.0 2.17e-01 100.0% 16.9%
3537096 377.1.1.16 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › zf-FCS 0.51 41.0 4.15e-01 100.0% 100.0%
5044292 375.11.1.0 ↗ few secondary structure elements › Rubredoxin-like › Zinc-binding domain in CopZ › Zinc-binding domain in CopZ 0.51 35.0 3.06e-01 87.5% 44.6%
3762289 386.1.1.106 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-FCS 0.51 41.0 4.13e-01 100.0% 100.0%