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YP_001604284.1

Arc-Vir

NC_010154__YP_001604284.1__AFV8-gp03__00003

Identity

Accession:
NC_010154 ↗
Protein ID:
YP_001604284.1 ↗
Kingdom:
archaea

Quality

86.2 mean pLDDT

Taxonomy

Zilligvirae› Taleaviricota› Tokiviricetes› Ligamenvirales› Lipothrixviridae› Betalipothrixvirus› Betalipothrixvirus_puteoliense

TaxID: 346884

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 4-79
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5mmiU01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.72 44.0 4.37e-01 100.0% 57.3%
2jheA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.71 42.0 4.12e-01 98.7% 54.3%
2rg4A01 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.69 60.0 4.47e-01 97.4% 87.6%
3n79A01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.68 39.0 3.90e-01 100.0% 55.1%
4u9rA02 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 40.0 4.36e-01 100.0% 70.8%
1wg1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.66 38.0 3.93e-01 100.0% 59.2%
4xaaA00 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.65 55.0 4.01e-01 96.1% 88.7%
3igqC00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.64 50.0 3.81e-01 100.0% 35.3%
4uxuA00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.64 53.0 3.77e-01 100.0% 31.9%
3nlcA01 3.30.70.2700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 43.0 4.40e-01 98.7% 72.4%
4afhE00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.62 51.0 3.70e-01 100.0% 32.1%
2p92A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.62 47.0 4.34e-01 80.3% 100.0%
3n2qA02 3.30.300.190 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.61 43.0 3.79e-01 73.7% 50.9%
2w8eA00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.61 49.0 3.63e-01 100.0% 33.0%
2bj0A00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.60 48.0 3.59e-01 100.0% 33.5%
3cjyA00 2.40.160.210 Mainly Beta › Beta Barrel › Porin › Acyl-CoA thioesterase, double hotdog domain 0.60 46.0 3.23e-01 84.2% 84.2%
4feuF01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 37.0 3.78e-01 100.0% 65.8%
4lviA01 3.30.930.30 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › 0.58 42.0 3.26e-01 100.0% 33.1%
2braA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.57 46.0 2.88e-01 90.8% 16.3%
2lxrA00 3.30.110.40 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › TusA-like domain 0.56 35.0 3.55e-01 100.0% 63.2%
8eisA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.55 44.0 3.39e-01 100.0% 35.0%
6fucA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.55 35.0 3.38e-01 100.0% 57.0%
3upsA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.55 43.0 3.82e-01 84.2% 81.5%
5jxsA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.54 40.0 3.34e-01 100.0% 42.3%
4h05B01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 34.0 3.24e-01 100.0% 53.8%
1dcoA00 3.30.1360.20 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Transcriptional coactivator/pterin dehydratase 0.54 37.0 3.40e-01 71.1% 66.7%
4mbrA01 2.60.40.1280 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 36.0 3.00e-01 100.0% 36.0%
1p6vA00 2.40.280.10 Mainly Beta › Beta Barrel › Small Protein B; Chain: A; › Small protein B 0.54 44.0 3.93e-01 100.0% 83.2%
2ip2A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 43.0 2.98e-01 100.0% 26.8%
3dh0B00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 37.0 2.80e-01 100.0% 28.9%
3q6oA02 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 41.0 3.79e-01 85.5% 76.7%
4fl4F02 2.60.40.4130 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 33.0 2.67e-01 100.0% 29.3%
4a9cA00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.53 45.0 3.13e-01 100.0% 29.1%
4v1al00 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.52 38.0 3.26e-01 80.3% 66.9%
4js8A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 35.0 3.38e-01 100.0% 60.7%
3fvcA03 2.30.29.100 Mainly Beta › Roll › PH-domain like › 0.51 44.0 3.94e-01 96.1% 93.6%
4n30A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 37.0 2.82e-01 76.3% 68.7%
3h8vB00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 36.0 2.54e-01 73.7% 77.5%
2ewhA01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.51 37.0 3.66e-01 80.3% 76.5%
1m55A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.51 45.0 3.39e-01 100.0% 86.5%
3n28A02 3.30.70.2020 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 34.0 3.12e-01 71.1% 65.1%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4006107 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.72 42.0 4.26e-01 98.7% 58.7%
3714955 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.69 58.0 3.96e-01 96.1% 60.2%
4543000 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.68 54.0 3.94e-01 100.0% 32.8%
3237142 5093.1.1.0 ↗ a+b complex topology › Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein › Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein › Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein 0.67 60.0 3.93e-01 100.0% 50.2%
5071707 304.19.1.4 ↗ a+b two layers › Alpha-beta plaits › eIF-2-alpha, C-terminal domain › eIF-2-alpha, C-terminal domain › DUF2110_N 0.66 44.0 4.51e-01 100.0% 70.7%
3436180 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.65 43.0 4.48e-01 100.0% 74.3%
3245167 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.65 54.0 3.83e-01 100.0% 30.9%
4256963 387.1.5.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like 0.64 41.0 4.65e-01 100.0% 98.0%
3795252 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.64 55.0 3.79e-01 100.0% 29.0%
3878682 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.63 50.0 3.63e-01 98.7% 31.0%
3220412 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.62 50.0 3.58e-01 100.0% 28.9%
4887532 244.1.1.9 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › GMC_oxred_C 0.62 44.0 3.33e-01 76.3% 73.5%
4034289 304.4.1.19 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › SCO4226-like 0.61 42.0 3.87e-01 100.0% 55.8%
4945414 304.12.1.0 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 0.60 42.0 4.01e-01 100.0% 62.2%
3228668 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.60 49.0 3.60e-01 100.0% 32.9%
4980724 304.165.1.4 ↗ a+b two layers › Alpha-beta plaits › Uncharacterized protein Ta1207 › Uncharacterized protein Ta1207 › HVO_2525_N 0.60 52.0 4.30e-01 100.0% 77.9%
1114935 2008.1.1.27 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAI1 0.59 49.0 3.30e-01 97.4% 98.5%
3394613 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.59 48.0 3.57e-01 100.0% 34.0%
4093835 2.21.1.1 ↗ beta barrels › OB-fold › Small protein B (SmpB) › Small protein B (SmpB) › SmpB 0.58 49.0 4.36e-01 100.0% 86.7%
2831758 2.21.1.1 ↗ beta barrels › OB-fold › Small protein B (SmpB) › Small protein B (SmpB) › SmpB 0.58 49.0 4.06e-01 100.0% 69.5%
4960068 2003.1.5.82 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.58 40.0 2.98e-01 100.0% 30.0%
3581195 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.56 48.0 3.61e-01 100.0% 45.7%
5040805 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.56 50.0 4.22e-01 98.7% 78.4%
5028094 304.20.1.4 ↗ a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.55 40.0 3.11e-01 98.7% 32.4%
3939423 11.12.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.54 46.0 3.25e-01 100.0% 30.4%
345204 2003.1.5.82 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.53 37.0 2.80e-01 100.0% 28.9%
5075991 304.6.1.1 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › FAD-oxidase_C 0.53 43.0 3.00e-01 90.8% 65.6%
3452716 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.53 46.0 3.09e-01 100.0% 31.6%
3218655 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.53 46.0 3.04e-01 100.0% 30.5%
3234427 206.1.1.78 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, Kinase-like 0.53 46.0 3.05e-01 100.0% 31.3%
4945563 210.1.4.1 ↗ a+b four layers › Ntn/PP2C › Ntn › (Glycosyl)asparaginase › Asparaginase_2 0.53 41.0 2.81e-01 88.2% 93.5%
3333828 206.1.1.20 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.53 47.0 3.05e-01 100.0% 33.1%
3426915 206.1.1.20 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.53 45.0 3.05e-01 100.0% 41.8%
4288657 304.11.1.0 ↗ a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase 0.52 35.0 3.56e-01 100.0% 69.3%
3924817 886.1.1.0 ↗ a+b duplicates or obligate multimers › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain 0.52 44.0 3.40e-01 96.1% 90.6%
3954949 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.52 46.0 3.02e-01 100.0% 27.3%
3368873 2008.2.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.51 28.0 2.40e-01 81.6% 28.8%
4008670 101.1.2.783 ↗ alpha arrays › HTH › HTH › winged helix domain › PF30336 0.51 38.0 3.96e-01 80.3% 94.3%
4017169 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.51 37.0 2.89e-01 80.3% 53.7%
4945701 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 38.0 3.66e-01 80.3% 76.5%
4047911 101.1.2.231 ↗ alpha arrays › HTH › HTH › winged helix domain › Staph_reg_Sar_Rot 0.50 36.0 3.15e-01 78.9% 92.3%