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YP_009725262.1

Arc-Vir

NC_003345__YP_009725262.1__HrrHF2-175__00034

Identity

Accession:
NC_003345 ↗
Protein ID:
YP_009725262.1 ↗
Kingdom:
archaea

Quality

78.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Thumleimavirales› Hafunaviridae› Haloferacalesvirus› Halorubrum_phage_HF2

TaxID: 33771

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 5-42
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3m7nA03 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.85 62.0 6.46e-01 86.8% 88.2%
2aklA01 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.72 56.0 5.49e-01 94.7% 79.1%
2xzm901 6.20.50.180 Special › Other non-globular › N-terminal domain of TfIIb › 0.71 52.0 4.28e-01 84.2% 43.1%
2nutB02 2.30.30.380 Mainly Beta › Roll › SH3 type barrels. › Zn-finger domain of Sec23/24 0.70 54.0 4.68e-01 86.8% 56.5%
2nutA02 2.30.30.380 Mainly Beta › Roll › SH3 type barrels. › Zn-finger domain of Sec23/24 0.69 53.0 4.63e-01 89.5% 63.9%
1m2vB03 2.30.30.380 Mainly Beta › Roll › SH3 type barrels. › Zn-finger domain of Sec23/24 0.68 53.0 4.61e-01 89.5% 59.7%
6bogA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.68 55.0 5.11e-01 97.4% 80.8%
1b7tA02 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.65 51.0 4.71e-01 89.5% 73.1%
2drpA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.62 41.0 4.27e-01 71.1% 76.5%
2kxqA01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.62 44.0 4.70e-01 86.8% 96.7%
4m4zA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.62 50.0 4.79e-01 97.4% 93.6%
5i4eA01 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.60 49.0 4.69e-01 97.4% 87.0%
2y8nB01 2.20.70.100 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.60 44.0 4.37e-01 97.4% 78.6%
2yshA01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.59 41.0 4.34e-01 84.2% 87.9%
2ysiA01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.59 42.0 4.43e-01 97.4% 90.9%
7pluA01 1.20.58.530 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 41.0 3.20e-01 86.8% 100.0%
2mdiA00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.58 45.0 4.08e-01 92.1% 75.0%
1kbeA00 3.30.60.20 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.58 41.0 3.93e-01 81.6% 85.7%
2do3A01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.56 43.0 4.11e-01 97.4% 80.4%
1tk7A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.56 38.0 3.92e-01 71.1% 94.6%
2dk7A00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.55 43.0 3.61e-01 100.0% 47.9%
4a2lF02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 40.0 2.50e-01 97.4% 19.4%
5cq2A02 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.54 43.0 4.21e-01 92.1% 86.0%
4w1vA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 37.0 2.57e-01 78.9% 79.1%
4fleA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 42.0 2.68e-01 94.7% 59.0%
3le4A00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.52 37.0 3.58e-01 92.1% 90.9%
2pvjA01 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.51 38.0 2.39e-01 84.2% 26.3%
2arzA02 3.20.180.10 Alpha Beta › Alpha-Beta Barrel › Split barrel-like › PNP-oxidase-like 0.51 37.0 3.18e-01 100.0% 72.7%
4nozB01 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.51 35.0 3.30e-01 76.3% 70.4%
4iiqC02 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.51 34.0 2.28e-01 71.1% 18.0%
6l4lA02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.50 40.0 2.78e-01 92.1% 68.4%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4975267 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.86 67.0 6.63e-01 89.5% 80.0%
4397965 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.84 67.0 4.44e-01 86.8% 23.6%
3255203 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.79 60.0 5.93e-01 92.1% 80.0%
4945128 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.77 62.0 6.42e-01 94.7% 100.0%
3498209 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.76 59.0 5.03e-01 86.8% 53.1%
4515794 375.1.1.11 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_S27 0.76 60.0 5.31e-01 86.8% 60.0%
3514931 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.76 58.0 5.80e-01 89.5% 82.5%
4962086 375.1.1.19 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › RNA_POL_M_15KD 0.76 59.0 5.87e-01 89.5% 82.5%
3741416 375.1.1.42 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rep_fac-A_C 0.75 54.0 5.71e-01 81.6% 100.0%
4938180 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.74 58.0 5.96e-01 97.4% 94.3%
3792293 375.1.1.30 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-Sec23_Sec24 0.73 57.0 4.42e-01 86.8% 41.2%
3258369 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.73 55.0 5.56e-01 89.5% 97.4%
2426645 375.8.1.1 ↗ few secondary structure elements › Rubredoxin-like › Zinc-binding domain of translation initiation factor 2 beta › Zinc-binding domain of translation initiation factor 2 beta › eIF-5_eIF-2B 0.72 58.0 5.18e-01 92.1% 69.1%
4947252 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.72 55.0 5.25e-01 86.8% 75.6%
None — 0.70 51.0 2.92e-01 78.9% 11.3%
3509582 375.1.1.184 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_TOP3B 0.70 57.0 3.75e-01 100.0% 47.6%
3717004 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.69 60.0 5.03e-01 97.4% 73.8%
3544109 2.1.1.133 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF4503 0.69 52.0 5.35e-01 92.1% 94.3%
3305631 375.1.1.184 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_TOP3B 0.69 55.0 4.59e-01 97.4% 93.3%
3656347 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.69 52.0 5.37e-01 86.8% 91.4%
5073392 606.1.1.0 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.68 49.0 3.70e-01 78.9% 97.9%
3741002 192.29.1.117 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Ima1_N 0.68 52.0 5.40e-01 86.8% 94.3%
3857437 375.1.1.184 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_TOP3B 0.68 51.0 5.09e-01 86.8% 82.5%
3525415 398.1.1.0 ↗ few secondary structure elements › Btk/CHORD zinc fingers › Btk/CHORD zinc fingers › Btk/CHORD zinc fingers 0.68 50.0 4.89e-01 86.8% 84.4%
3715847 375.1.1.184 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_TOP3B 0.68 55.0 4.08e-01 100.0% 92.7%
3251327 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.67 50.0 4.58e-01 86.8% 61.8%
3333753 375.1.1.42 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rep_fac-A_C 0.67 53.0 5.44e-01 89.5% 100.0%
3815420 376.1.2.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain 0.66 51.0 4.69e-01 92.1% 100.0%
3699533 2.1.1.42 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Rep_fac-A_C 0.66 55.0 3.52e-01 100.0% 33.2%
5066735 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.65 53.0 4.90e-01 89.5% 68.0%
3517444 375.10.1.0 ↗ few secondary structure elements › Rubredoxin-like › Zinc finger domain of DNA polymerase-alpha › Zinc finger domain of DNA polymerase-alpha 0.65 52.0 4.46e-01 97.4% 69.1%
3678606 375.1.1.212 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_FGT1_2 0.64 50.0 5.12e-01 89.5% 94.3%
4979347 375.1.3.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 0.64 51.0 4.26e-01 97.4% 50.0%
4997767 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.63 52.0 4.97e-01 97.4% 80.0%
3575430 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.62 47.0 4.42e-01 86.8% 66.0%
5070745 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.61 49.0 4.70e-01 92.1% 73.3%
3919418 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.61 43.0 4.50e-01 86.8% 100.0%
3297722 64.1.1.0 ↗ beta meanders › WW domain-like › WW domain › WW domain 0.60 47.0 4.78e-01 100.0% 100.0%
3958082 7577.1.1.0 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases 0.60 41.0 2.45e-01 84.2% 8.6%
3598119 330.3.1.0 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like 0.58 41.0 3.49e-01 76.3% 44.3%
4028249 330.3.1.0 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like 0.57 42.0 3.80e-01 76.3% 55.6%
5016488 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.57 43.0 3.95e-01 97.4% 93.3%
5032233 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 44.0 3.21e-01 94.7% 62.6%
3394681 252.1.1.1 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.53 40.0 3.90e-01 100.0% 80.0%
3586791 64.1.1.0 ↗ beta meanders › WW domain-like › WW domain › WW domain 0.53 40.0 4.15e-01 97.4% 97.1%
299936 233.1.1.3 ↗ a+b two layers › MHC antigen-recognition domain › MHC antigen-recognition domain › MHC antigen-recognition domain › MHC_II_alpha 0.53 36.0 2.86e-01 71.1% 34.1%