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dnapol_B

Euk-Vir

Oryctes_rhinoceros_nudivirus

dnapol_B__YP_002321312__Oryctes_rhinoceros_nudivirus__92521

Identity

Accession:
YP_002321312 ↗
Protein ID:
dnapol_B
Kingdom:
euk

Quality

60.2 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Nudiviridae› Alphanudivirus› Oryctes_rhinoceros_nudivirus

TaxID: 92521

Cluster

View cluster (4 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 217-448
PDB
Domain cluster: rep: DNA_polymerase_B__YP_009553129__Drosophila_innubila_nudivirus__2057187__D260-512
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03104.26 best DNA_pol_B_exo1 34.2 2.50e-08 72.4% 73.1%
D2 medium residues 11-75_194-214
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1jegA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.70 39.0 4.52e-01 75.6% 76.7%
1rl2A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.65 42.0 4.89e-01 74.4% 100.0%
2fhdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.64 37.0 4.21e-01 73.3% 79.0%
3kf6A00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.63 43.0 3.75e-01 72.1% 83.1%
1tg0A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.62 36.0 4.03e-01 76.7% 74.2%
1x6oA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.62 43.0 4.51e-01 73.3% 100.0%
1vq8A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.61 41.0 4.28e-01 74.4% 75.6%
6jy5B00 2.40.50.220 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › EutN/Ccml 0.60 41.0 4.25e-01 70.9% 96.3%
2pi2D00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.60 41.0 3.71e-01 72.1% 83.7%
1f9qD00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.59 43.0 4.67e-01 93.0% 100.0%
2gfaB01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.59 35.0 4.02e-01 73.3% 82.3%
2qggA02 2.30.30.240 Mainly Beta › Roll › SH3 type barrels. › PRC-barrel domain 0.58 38.0 3.92e-01 72.1% 69.9%
5cbeE00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.57 39.0 4.36e-01 89.5% 95.3%
5zg8A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 40.0 3.80e-01 74.4% 86.3%
3u4zA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 41.0 3.87e-01 79.1% 83.5%
1icwB00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 39.0 4.26e-01 83.7% 95.5%
1p16B02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 40.0 3.49e-01 76.7% 69.9%
4v0bA00 3.30.720.210 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.55 36.0 4.03e-01 81.4% 92.1%
4gyiA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 31.0 2.99e-01 98.8% 49.0%
3c96A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 34.0 2.82e-01 72.1% 33.3%
6gbuD00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.50 29.0 3.20e-01 76.7% 71.9%
ECOD (57)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3931602 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.68 38.0 4.17e-01 74.4% 67.1%
4028381 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.65 45.0 4.21e-01 83.7% 58.1%
4222760 4.6.1.6 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain › PRC_RimM 0.65 40.0 4.34e-01 73.3% 74.3%
4399169 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.65 42.0 4.83e-01 70.9% 93.3%
3228213 4.8.1.2 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.64 37.0 4.20e-01 72.1% 75.4%
5035086 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.64 43.0 4.99e-01 79.1% 100.0%
4161673 4.1.1.105 ↗ beta barrels › SH3 › SH3 › SH3 › DUF5604 0.62 35.0 3.54e-01 72.1% 54.1%
4307191 4.6.1.6 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain › PRC_RimM 0.62 38.0 3.96e-01 70.9% 65.0%
1411292 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.62 44.0 3.89e-01 74.4% 84.7%
4380251 2.4.1.7 ↗ beta barrels › OB-fold › MOP-like › MOP-like › OB_MalK 0.62 42.0 3.80e-01 70.9% 84.2%
3709493 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.62 42.0 3.68e-01 93.0% 46.2%
4504508 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.61 43.0 4.41e-01 84.9% 75.3%
4962316 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.61 44.0 3.82e-01 75.6% 80.8%
4341478 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.61 43.0 4.37e-01 84.9% 75.3%
5054268 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.60 43.0 4.80e-01 84.9% 98.5%
4190716 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.60 43.0 3.89e-01 74.4% 83.5%
3694693 4.8.1.2 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.60 39.0 4.36e-01 74.4% 87.7%
4598956 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.60 44.0 4.16e-01 89.5% 63.8%
4443040 2.4.1.1 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE 0.60 41.0 3.88e-01 70.9% 86.5%
4451633 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.60 41.0 3.58e-01 70.9% 89.2%
4646663 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.60 41.0 3.54e-01 70.9% 83.7%
4234366 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.60 41.0 3.63e-01 70.9% 91.2%
4623446 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.59 40.0 3.62e-01 70.9% 90.3%
5081103 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.59 41.0 3.63e-01 70.9% 85.6%
4940372 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.59 43.0 4.68e-01 79.1% 94.3%
4103327 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.59 41.0 3.67e-01 72.1% 91.1%
5032554 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.59 40.0 3.60e-01 70.9% 86.4%
4235194 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.59 41.0 3.70e-01 74.4% 82.4%
4073602 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.59 40.0 3.73e-01 70.9% 89.1%
4998346 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.58 40.0 3.54e-01 70.9% 83.8%
4984320 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.58 41.0 3.63e-01 74.4% 86.9%
4944505 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.58 40.0 3.65e-01 72.1% 89.2%
3941442 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.58 41.0 3.66e-01 74.4% 90.6%
4411951 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.58 41.0 3.59e-01 74.4% 72.6%
3936225 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 35.0 3.75e-01 82.6% 71.4%
4281449 2.4.1.3 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2,OB_MalK 0.58 41.0 3.66e-01 75.6% 85.9%
4391061 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.58 41.0 3.71e-01 74.4% 90.8%
4396749 4.6.1.6 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain › PRC_RimM 0.58 36.0 3.78e-01 73.3% 69.3%
4371403 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.58 40.0 3.74e-01 72.1% 90.9%
4236900 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.58 41.0 3.61e-01 74.4% 89.1%
4944219 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.58 40.0 3.54e-01 72.1% 87.2%
4446834 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.58 41.0 3.75e-01 74.4% 85.0%
4052370 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.57 40.0 4.43e-01 72.1% 100.0%
4998344 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.57 40.0 3.54e-01 74.4% 82.1%
3973121 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.57 40.0 3.58e-01 74.4% 90.6%
3620698 2.6.1.0 ↗ beta barrels › OB-fold › Staphylococcal nuclease › Staphylococcal nuclease 0.57 42.0 4.14e-01 79.1% 87.4%
4079201 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.57 40.0 3.73e-01 74.4% 90.9%
4309833 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.57 40.0 3.56e-01 74.4% 90.6%
4951344 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.57 40.0 3.68e-01 74.4% 90.4%
4346153 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.57 40.0 3.49e-01 74.4% 91.9%
3948546 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.56 40.0 3.83e-01 74.4% 88.0%
4951352 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.56 40.0 3.59e-01 74.4% 90.8%
3985171 2.4.1.1 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE 0.56 40.0 3.43e-01 74.4% 91.4%
4951333 2.4.1.1 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE 0.55 38.0 3.47e-01 73.3% 87.5%
4633023 2.4.1.1 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE 0.55 38.0 3.31e-01 73.3% 90.7%
3260945 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.51 32.0 3.65e-01 74.4% 90.0%
3587789 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.51 36.0 3.43e-01 75.6% 80.0%
D3 medium residues 76-161
PDB
D4 medium residues 582-675
PDB