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URC16917.1

Arc-Vir

ON548425__URC16917.1__X__00163

Identity

Accession:
ON548425 ↗
Protein ID:
URC16917.1 ↗
Kingdom:
archaea

Quality

84.4 mean pLDDT

Taxonomy

Helarchaeota_virus_Nidhogg_Meg22_1012

TaxID: 2946032

Cluster

View cluster (3 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 high residues 1-172
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5of3A00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.81 70.0 5.56e-01 90.1% 69.6%
4bpuC00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.79 72.0 5.50e-01 96.5% 82.3%
2faoA01 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.76 71.0 5.96e-01 100.0% 91.5%
4limA00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.76 69.0 5.22e-01 96.5% 82.7%
2atzA00 3.90.920.20 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › HP0184-like 0.75 55.0 5.53e-01 95.9% 73.3%
3h20A02 3.30.70.1790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RepB DNA-primase, N-terminal domain 0.75 45.0 5.73e-01 77.3% 100.0%
1itpA00 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.64 29.0 4.13e-01 78.5% 92.2%
2bj3D02 3.30.70.1150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2 0.63 30.0 4.19e-01 79.1% 93.8%
1z1dB00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.63 42.0 4.80e-01 89.0% 89.3%
4i68A00 3.30.70.1800 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 31.0 4.14e-01 86.0% 88.9%
2xhcA01 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.63 35.0 4.50e-01 71.5% 96.8%
5t0oA02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.60 36.0 4.57e-01 82.6% 100.0%
1q5yC00 3.30.70.1150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2 0.59 29.0 4.00e-01 79.1% 95.1%
1wvfA03 3.40.462.10 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain 0.59 43.0 3.96e-01 75.6% 81.8%
5yppA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.59 33.0 4.23e-01 70.3% 100.0%
1m55A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.58 41.0 3.99e-01 72.1% 94.8%
3to8A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.58 36.0 4.37e-01 77.3% 100.0%
2dbbA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.58 32.0 4.11e-01 82.0% 96.8%
2b4vA03 3.30.70.1970 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 32.0 4.08e-01 87.8% 91.9%
1f08B00 3.40.1310.10 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.58 41.0 4.43e-01 91.3% 85.5%
1sjrA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.58 35.0 4.23e-01 84.3% 93.5%
1r9wA00 3.40.1310.10 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.58 39.0 4.25e-01 90.1% 83.3%
3rjaA02 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.57 43.0 3.94e-01 78.5% 68.6%
2efpA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.57 30.0 3.74e-01 73.8% 85.7%
1tdjA03 3.40.1020.10 Alpha Beta › 3-Layer(aba) Sandwich › Biosynthetic Threonine Deaminase; domain 3 › Biosynthetic Threonine Deaminase; Domain 3 0.56 41.0 4.22e-01 73.8% 82.0%
3kdgA02 3.30.1370.100 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › MutL, C-terminal domain, regulatory subdomain 0.54 28.0 3.63e-01 90.7% 89.4%
4f67A01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 31.0 3.73e-01 70.9% 88.7%
1pbuA00 3.30.70.1010 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Translation elongation factor EF1B, gamma chain, conserved domain 0.51 38.0 3.97e-01 92.4% 83.3%
1x4dA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.51 30.0 3.70e-01 88.4% 96.1%
ECOD (57)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5081312 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.88 84.0 7.64e-01 100.0% 84.5%
5029237 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.86 75.0 6.48e-01 90.1% 71.4%
4085259 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.84 73.0 6.19e-01 90.1% 82.3%
4942021 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.84 80.0 6.67e-01 100.0% 78.2%
5065288 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.84 73.0 6.08e-01 90.1% 71.3%
5019731 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.83 72.0 5.71e-01 90.1% 82.8%
4973338 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.83 72.0 5.94e-01 90.1% 78.9%
5045979 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.83 72.0 6.05e-01 90.1% 65.2%
4993038 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.83 72.0 6.10e-01 90.1% 73.9%
4552974 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.83 72.0 6.30e-01 90.1% 79.6%
4426711 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.83 72.0 6.15e-01 90.1% 67.8%
4425840 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.83 71.0 5.67e-01 90.1% 83.4%
5051647 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.83 71.0 6.24e-01 89.5% 76.7%
5044094 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.82 72.0 6.39e-01 90.1% 77.0%
5037338 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.82 78.0 6.61e-01 100.0% 91.7%
5027616 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.82 71.0 6.06e-01 90.1% 65.0%
4972968 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.82 70.0 5.98e-01 90.1% 73.2%
4946939 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.82 70.0 6.63e-01 89.5% 88.0%
4554731 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.82 71.0 6.38e-01 91.3% 79.1%
4442634 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.81 71.0 5.78e-01 90.1% 82.1%
4983703 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.81 77.0 6.53e-01 100.0% 78.9%
5069642 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.81 70.0 6.40e-01 90.1% 78.2%
4956744 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.81 70.0 6.04e-01 90.1% 81.6%
4099067 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.81 70.0 5.99e-01 90.1% 72.7%
4998612 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.81 69.0 6.09e-01 89.5% 75.8%
4955551 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.80 76.0 6.63e-01 100.0% 80.8%
3278096 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.79 71.0 5.69e-01 94.8% 58.4%
4987159 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.79 73.0 6.27e-01 97.7% 66.5%
3921299 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.79 72.0 5.80e-01 95.9% 76.8%
4986859 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.78 74.0 6.07e-01 100.0% 68.1%
3692641 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.78 72.0 5.94e-01 96.5% 76.7%
2711606 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.78 74.0 5.80e-01 100.0% 59.8%
3284431 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.78 74.0 5.92e-01 100.0% 62.6%
None — 0.78 70.0 5.63e-01 94.8% 60.0%
4962169 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.77 65.0 5.76e-01 90.1% 64.2%
5004945 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.77 67.0 5.72e-01 89.5% 69.4%
4960009 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.77 71.0 5.93e-01 98.3% 67.0%
None — 0.77 73.0 5.85e-01 100.0% 63.5%
1779551 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.76 71.0 5.86e-01 100.0% 67.8%
7175 862.1.1.2 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DUF1882 0.75 55.0 5.53e-01 95.9% 73.3%
5004385 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.73 63.0 5.68e-01 89.5% 73.2%
3989046 862.1.1.8 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › AEP-TOTE 0.69 64.0 5.85e-01 100.0% 75.6%
143128 304.55.1.4 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › T_Ag_DNA_bind 0.67 42.0 4.97e-01 87.8% 90.8%
5063265 304.8.1.4 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › NikR_C 0.63 28.0 4.10e-01 78.5% 94.7%
5051000 304.8.1.4 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › NikR_C 0.62 29.0 3.97e-01 78.5% 89.2%
3206066 327.19.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › DNA mismatch repair protein MutL regulatory subdomain › DNA mismatch repair protein MutL regulatory subdomain 0.60 31.0 3.89e-01 81.4% 79.1%
3291661 304.6.1.3 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.57 43.0 3.85e-01 78.5% 60.0%
5051739 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.57 40.0 2.81e-01 70.9% 90.9%
4043242 304.6.1.5 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › Cytokin-bind 0.56 41.0 3.70e-01 76.2% 61.7%
4967469 304.110.1.1 ↗ a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like › Acylphosphatase 0.55 35.0 4.17e-01 75.6% 94.8%
4944621 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.55 35.0 4.03e-01 89.5% 88.8%
5049083 304.37.1.0 ↗ a+b two layers › Alpha-beta plaits › Sulfite reductase, domains 1 and 3 › Sulfite reductase, domains 1 and 3 0.54 44.0 3.94e-01 85.5% 72.7%
4984065 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.54 31.0 3.78e-01 80.8% 87.3%
3603835 304.122.1.1 ↗ a+b two layers › Alpha-beta plaits › Nitrogen repressor-like proteins › Nitrogen repressor-like proteins › NRD1_2 0.54 32.0 3.88e-01 77.9% 93.3%
5052911 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.52 39.0 2.91e-01 78.5% 93.1%
5009932 131.1.1.0 ↗ alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like 0.51 43.0 3.38e-01 89.5% 91.9%
3196763 304.6.1.3 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.51 39.0 3.37e-01 80.8% 82.5%
D2 high residues 192-303
PDB
Domain cluster: rep: IMGVR_UViG_3300021587_000002-3300021587-Ga0190351_10000101__D28-116
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3dA03 1.10.579.10 Mainly Alpha › Orthogonal Bundle › DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 › DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 0.72 66.0 5.41e-01 97.3% 78.9%
3h20A04 1.10.1240.50 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.63 46.0 5.15e-01 100.0% 95.5%
2rq1A00 1.20.80.10 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.60 44.0 4.52e-01 76.8% 85.3%
4ol9A02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.55 43.0 4.14e-01 83.9% 97.6%
6s6hA01 1.10.10.2830 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.52 32.0 3.29e-01 76.8% 62.4%
3go9A02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.51 37.0 3.07e-01 77.7% 78.3%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5054621 182.1.3.0 ↗ alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX 0.76 68.0 6.55e-01 97.3% 92.8%
5030284 182.1.3.3 ↗ alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.75 65.0 6.41e-01 92.9% 99.2%
5058298 182.1.3.0 ↗ alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX 0.73 66.0 6.50e-01 97.3% 97.5%
5064030 182.1.3.0 ↗ alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX 0.70 55.0 5.94e-01 83.0% 98.9%
4380725 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.65 37.0 4.39e-01 70.5% 82.7%
4960595 101.1.1.549 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DDE_Tnp_1_5 0.60 41.0 4.79e-01 80.4% 100.0%
4218930 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.53 33.0 3.88e-01 95.5% 93.3%
3227955 2484.8.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Separase pseudo-protease domain (PPD) › Separase pseudo-protease domain (PPD) › Peptidase_C50 0.52 46.0 3.54e-01 99.1% 75.8%