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DNA-binding_protein

Euk-Vir

Pigeon_adenovirus_2

DNA-binding_protein__YP_009310439__Pigeon_adenovirus_2__1907767

Identity

Accession:
YP_009310439 ↗
Protein ID:
DNA-binding_protein
Kingdom:
euk

Quality

72.1 mean pLDDT

Taxonomy

Bamfordvirae› Preplasmiviricota› Pharingeaviricetes› Rowavirales› Adenoviridae› Aviadenovirus› Pigeon_adenovirus_2

TaxID: 1907767

Cluster

View cluster (53 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 medium residues 135-204
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02236.24 best Viral_DNA_bi 86.9 1.40e-24 100.0% 88.6%
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1m6nA04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.74 50.0 3.99e-01 100.0% 36.3%
6tmfT00 1.10.60.20 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Ribosomal protein S17 0.73 44.0 4.65e-01 92.9% 67.2%
2ipcA04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.71 48.0 3.29e-01 100.0% 20.2%
1nktA04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.69 46.0 3.48e-01 100.0% 27.7%
2fsfB04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.69 46.0 3.30e-01 100.0% 23.1%
3f75P00 1.10.287.2250 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.66 43.0 4.21e-01 71.4% 61.3%
7cosB02 1.10.1140.10 Mainly Alpha › Orthogonal Bundle › Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 › Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 0.64 37.0 3.57e-01 100.0% 50.6%
1j1vA00 1.10.1750.10 Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain 0.62 39.0 3.54e-01 100.0% 46.8%
2looA02 1.10.10.1740 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Transmembrane protein 14-like 0.61 41.0 4.07e-01 94.3% 65.3%
1hbgA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.61 47.0 3.78e-01 100.0% 40.8%
1w0bA01 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.58 42.0 3.85e-01 100.0% 57.6%
3keyA01 1.10.10.1080 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Stn1, N-terminal wHTH domain 0.58 48.0 4.49e-01 92.9% 80.5%
7e84A03 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 39.0 3.31e-01 71.4% 60.2%
1cg5B00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.57 47.0 3.78e-01 100.0% 45.4%
4m70B00 1.10.246.200 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › WPP domain 0.57 44.0 4.06e-01 100.0% 64.8%
7vwtA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.57 46.0 3.09e-01 94.3% 42.2%
3k3uA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.56 47.0 3.80e-01 100.0% 48.2%
6o0aA01 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.56 44.0 3.58e-01 100.0% 43.0%
2wg7A00 1.20.90.10 Mainly Alpha › Up-down Bundle › Phospholipase A2 › Phospholipase A2 domain 0.56 36.0 3.01e-01 94.3% 37.2%
7lb8B01 1.10.3470.10 Mainly Alpha › Orthogonal Bundle › ABC transporter involved in vitamin B12 uptake, BtuC › ABC transporter involved in vitamin B12 uptake, BtuC 0.55 46.0 3.08e-01 97.1% 99.4%
4bbrM00 1.10.472.170 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › 0.55 40.0 2.95e-01 78.6% 52.3%
2rkhA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.54 38.0 3.75e-01 100.0% 68.4%
3on3B00 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.53 40.0 3.01e-01 80.0% 60.6%
3d2yA02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.52 36.0 3.43e-01 91.4% 59.5%
2rkkA01 1.25.40.270 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Vacuolar protein sorting-associated protein vta1 0.52 38.0 3.02e-01 80.0% 82.7%
2m4eA00 1.20.120.1930 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Uncharacterised protein PF16691 family 0.52 44.0 4.17e-01 98.6% 87.2%
4nx8B00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.51 41.0 2.87e-01 91.4% 71.4%
4u04A02 1.10.3290.10 Mainly Alpha › Orthogonal Bundle › Fic-like fold › Fido-like domain 0.51 44.0 3.15e-01 100.0% 91.3%
2fgyA01 1.20.120.1310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain 0.51 45.0 3.93e-01 100.0% 75.7%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.50 38.0 3.55e-01 78.6% 91.8%
4dxkA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.50 44.0 3.65e-01 97.1% 78.4%
5jc3A02 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.50 43.0 3.64e-01 100.0% 89.7%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1118996 510.1.1.1 ↗ alpha bundles › Domain of early E2A DNA-binding protein, ADDBP › Domain of early E2A DNA-binding protein, ADDBP › Domain of early E2A DNA-binding protein, ADDBP › Viral_DNA_bi 0.92 86.0 7.80e-01 100.0% 82.2%
3195747 3788.1.1.0 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) 0.67 47.0 4.73e-01 100.0% 74.3%
5009834 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.64 46.0 4.18e-01 100.0% 56.8%
4051167 106.1.1.1 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › Globin 0.61 48.0 3.78e-01 100.0% 41.2%
3704855 2003.1.9.8 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF, E1_4HB 0.60 49.0 3.38e-01 91.4% 27.6%
4382271 3949.1.1.1 ↗ alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › IPPT 0.59 51.0 3.61e-01 100.0% 83.9%
3968965 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.59 36.0 3.32e-01 100.0% 47.8%
3744227 193.1.1.1 ↗ alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like › CH 0.59 49.0 4.04e-01 98.6% 70.7%
5029389 601.17.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Group V grass pollen allergen › Group V grass pollen allergen 0.57 44.0 3.55e-01 85.7% 50.3%
4569135 192.29.1.274 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › NifW 0.57 40.0 3.78e-01 100.0% 60.0%
4004067 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 34.0 3.24e-01 100.0% 50.6%
3584048 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 37.0 3.41e-01 100.0% 53.3%
3699643 6155.1.1.1 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › MtN3_slv 0.56 34.0 3.22e-01 100.0% 50.6%
4014199 193.1.1.0 ↗ alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like 0.56 45.0 4.14e-01 95.7% 88.0%
4025161 6155.1.1.1 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › MtN3_slv 0.55 34.0 3.27e-01 100.0% 53.8%
3186578 101.38.1.2 ↗ alpha arrays › HTH › DNA-binding domain of the replication initiator protein ColE2-Rep › DNA-binding domain of the replication initiator protein ColE2-Rep › DUF7721 0.55 46.0 3.73e-01 94.3% 47.9%
5055868 6155.1.1.2 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.54 37.0 3.64e-01 100.0% 65.3%
5014720 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.54 40.0 2.88e-01 77.1% 40.0%
3228201 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.54 45.0 3.41e-01 94.3% 84.3%
4994067 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.54 40.0 3.60e-01 98.6% 56.0%
3361553 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.54 36.0 3.42e-01 98.6% 57.6%
3394903 108.2.1.1 ↗ alpha arrays › EF-hand › Insect pheromone/odorant-binding proteins › Insect pheromone/odorant-binding proteins › PBP_GOBP 0.53 41.0 3.79e-01 88.6% 100.0%
3536798 633.24.1.4 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › RIN1 0.50 40.0 3.62e-01 90.0% 74.0%
D2 medium residues 321-406_422-471
PDB
Domain cluster: rep: DBP__YP_009162599__Skunk_adenovirus_PB1__1641642__D183-206_246-418
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03728.19 best Viral_DNA_Zn_bi 70.5 2.10e-19 63.2% 93.9%