←Back to structures

YP_010355857.1

Arc-Vir

NC_062738__YP_010355857.1__M1M16-gp14__00014

Identity

Accession:
NC_062738 ↗
Protein ID:
YP_010355857.1 ↗
Kingdom:
archaea

Quality

76.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Methanobavirales› Anaerodiviridae› Metforvirus› Methanobacterium_virus_Drs3

TaxID: 1430441

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 high residues 3-64
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1r79A01 3.30.60.20 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.76 50.0 5.27e-01 82.3% 76.4%
3lrqB00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.76 51.0 4.71e-01 80.6% 55.0%
1wimA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.75 52.0 4.56e-01 87.1% 47.9%
2lxhC00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.75 45.0 4.63e-01 82.3% 63.8%
2cklB01 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.75 48.0 4.61e-01 75.8% 57.7%
2lgvA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.71 50.0 4.14e-01 72.6% 54.0%
4wz2C00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.70 45.0 4.23e-01 77.4% 54.1%
2jrjA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.69 43.0 4.64e-01 77.4% 76.9%
1zbdB00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.68 51.0 4.01e-01 88.7% 39.8%
4ccgY00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.68 47.0 4.63e-01 82.3% 67.2%
2kkxA00 3.30.40.80 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Effector protein NleG 0.67 50.0 4.25e-01 87.1% 49.0%
3m3kA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.67 35.0 2.65e-01 87.1% 21.2%
3t7lA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.62 45.0 4.27e-01 85.5% 64.9%
5y20A00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.61 43.0 4.72e-01 74.2% 98.1%
1z6uA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.61 53.0 4.34e-01 96.8% 65.2%
4nn2B00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.61 46.0 3.82e-01 83.9% 100.0%
4qf3A00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.59 39.0 4.09e-01 77.4% 75.4%
4zohA05 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.59 39.0 3.01e-01 91.9% 28.8%
2co8A00 2.10.110.10 Mainly Beta › Ribbon › Cysteine Rich Protein › Cysteine Rich Protein 0.58 45.0 4.20e-01 93.5% 65.9%
8be0A01 3.40.91.90 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain 0.58 41.0 2.92e-01 74.2% 68.6%
2qgpA00 1.10.30.50 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › 0.58 45.0 4.10e-01 85.5% 68.7%
2eqpA00 4.10.400.20 Few Secondary Structures › Irregular › Low-density Lipoprotein Receptor › 0.54 32.0 3.42e-01 77.4% 68.0%
2q07A02 3.10.450.90 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › ArcTGT, C2 domain 0.54 38.0 3.78e-01 77.4% 87.7%
3w6kC00 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 0.53 41.0 3.77e-01 87.1% 98.9%
2ysmA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.53 36.0 3.05e-01 85.5% 39.6%
2innB00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.52 45.0 2.72e-01 100.0% 47.9%
2oap202 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 39.0 2.58e-01 82.3% 76.5%
3hcsA02 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.51 33.0 3.51e-01 90.3% 78.8%
6qv3A05 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 0.51 33.0 2.92e-01 85.5% 45.2%
ECOD (71)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4970980 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.82 57.0 5.75e-01 87.1% 71.4%
3700252 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.82 52.0 5.51e-01 75.8% 72.7%
3224677 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.82 54.0 5.51e-01 74.2% 70.0%
3928741 376.1.1.27 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_5 0.81 51.0 4.58e-01 77.4% 47.1%
5049855 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.81 54.0 5.55e-01 79.0% 71.7%
3614502 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.81 56.0 4.81e-01 72.6% 85.3%
5071927 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.81 56.0 5.90e-01 80.6% 81.8%
4022452 376.1.1.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4 0.79 50.0 4.17e-01 77.4% 38.1%
3993220 376.1.2.24 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › RH_dom 0.78 55.0 5.83e-01 80.6% 83.6%
4975289 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.77 54.0 5.50e-01 79.0% 75.0%
3764525 632.6.1.7 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit › RH_dom 0.77 50.0 5.45e-01 74.2% 82.0%
3928472 376.1.1.95 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › RH_dom 0.77 55.0 5.49e-01 80.6% 72.3%
3380774 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.77 56.0 5.65e-01 85.5% 76.2%
3295801 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.77 52.0 4.58e-01 83.9% 48.9%
3543125 4044.1.1.12 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › RH_dom 0.76 50.0 5.49e-01 75.8% 84.0%
3888986 376.1.1.95 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › RH_dom 0.76 50.0 5.46e-01 74.2% 84.0%
3620819 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.76 48.0 4.91e-01 72.6% 66.7%
3999619 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.76 49.0 5.31e-01 74.2% 82.0%
3497361 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.76 50.0 5.38e-01 80.6% 84.0%
3583761 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.76 48.0 5.32e-01 72.6% 83.3%
3230733 376.1.2.24 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › RH_dom 0.76 49.0 4.97e-01 72.6% 68.3%
3233552 376.1.1.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4 0.75 48.0 5.21e-01 82.3% 80.0%
3406028 4044.1.1.12 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › RH_dom 0.75 50.0 5.09e-01 75.8% 70.0%
3480673 375.4.1.0 ↗ few secondary structure elements › Rubredoxin-like › Nucleolar RNA-binding protein Nop10-like › Nucleolar RNA-binding protein Nop10-like 0.75 51.0 5.57e-01 72.6% 88.0%
3233807 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.75 47.0 4.57e-01 72.6% 57.1%
3825851 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.74 56.0 5.34e-01 79.0% 80.0%
3728775 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.74 54.0 4.87e-01 98.4% 56.5%
4011161 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.74 55.0 5.25e-01 85.5% 68.6%
3318393 376.1.1.20 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_UBOX 0.73 54.0 4.63e-01 79.0% 50.5%
3915745 376.1.1.119 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › PF26037 0.73 50.0 5.45e-01 75.8% 88.0%
3926399 376.1.1.95 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › RH_dom 0.73 47.0 5.16e-01 74.2% 82.0%
3370105 376.1.3.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD 0.73 52.0 5.28e-01 74.2% 96.7%
3671431 376.1.1.40 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_11 0.72 45.0 5.16e-01 80.6% 88.9%
5049922 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.72 51.0 5.19e-01 88.7% 76.7%
3187970 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.71 49.0 5.02e-01 74.2% 75.0%
3592489 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.71 54.0 5.33e-01 80.6% 80.0%
3492870 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.70 52.0 5.50e-01 82.3% 87.3%
5076504 376.1.1.183 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › Prok-RING_1 0.70 52.0 5.68e-01 95.2% 98.0%
2327296 376.1.1.10 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › T3SS_NleG 0.69 52.0 4.20e-01 87.1% 44.5%
3597540 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.69 60.0 3.75e-01 98.4% 35.4%
3232804 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.68 46.0 4.93e-01 71.0% 80.0%
3484821 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.68 48.0 4.73e-01 74.2% 95.4%
3914982 377.1.1.5 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › LIM 0.68 51.0 5.17e-01 82.3% 83.3%
3906009 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.67 53.0 4.61e-01 91.9% 55.0%
3360937 376.1.1.95 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › RH_dom 0.66 50.0 5.30e-01 80.6% 98.2%
3830925 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.66 48.0 4.96e-01 77.4% 81.7%
None — 0.66 56.0 4.98e-01 91.9% 74.1%
3938423 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.66 43.0 4.61e-01 83.9% 83.7%
3610348 376.1.2.23 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › PF26235 0.65 44.0 4.20e-01 82.3% 58.7%
3529744 376.1.1.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4 0.64 54.0 4.33e-01 95.2% 50.4%
3766928 376.1.1.20 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_UBOX 0.64 53.0 4.33e-01 95.2% 50.8%
3237227 376.1.1.103 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_Vps41 0.64 50.0 4.79e-01 85.5% 74.3%
2322754 376.1.2.3 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_4 0.64 49.0 4.68e-01 88.7% 71.6%
3891072 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.64 53.0 4.67e-01 95.2% 62.1%
5052355 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.64 50.0 4.19e-01 85.5% 57.1%
3828930 376.1.2.2 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_2 0.63 43.0 4.39e-01 80.6% 73.3%
3305271 376.1.1.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4 0.63 50.0 4.48e-01 88.7% 77.8%
5075724 376.1.1.181 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › Zn_Ribbon_1 0.63 52.0 5.29e-01 88.7% 91.7%
3916229 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.63 47.0 4.47e-01 80.6% 68.0%
3863057 632.11.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › RH_dom 0.63 54.0 4.04e-01 96.8% 63.9%
3798139 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.62 47.0 4.15e-01 83.9% 98.9%
5051552 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.62 47.0 4.00e-01 85.5% 51.0%
3371462 376.1.3.25 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD-1st_NSD 0.62 44.0 3.30e-01 74.2% 38.7%
3886848 377.9.1.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › HIT/MYND zinc finger-like › HIT/MYND zinc finger-like › zf-MYND 0.61 42.0 4.43e-01 79.0% 81.8%
3616025 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 34.0 2.37e-01 91.9% 16.5%
3242125 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.56 45.0 3.06e-01 91.9% 24.7%
4949181 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.56 43.0 4.11e-01 85.5% 72.0%
6441 243.6.1.8 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain › AF_0587-like_pre-PUA 0.55 38.0 3.83e-01 77.4% 87.9%
3739835 386.1.1.12 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › Sgf11 0.52 34.0 3.09e-01 87.1% 46.7%
3701829 7015.1.1.1 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › DHHC 0.52 42.0 3.08e-01 96.8% 71.7%
389331 386.1.1.13 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › Sgf11,Sgf11_N 0.52 34.0 3.03e-01 88.7% 45.2%