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alkaline_exonuclease

Euk-Vir

Neodiprion_abietis_NPV

alkaline_exonuclease__YP_667884__Neodiprion_abietis_NPV__204507

Identity

Accession:
YP_667884 ↗
Protein ID:
alkaline_exonuclease
Kingdom:
euk

Quality

78.4 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Gammabaculovirus› Neodiprion_abietis_nucleopolyhedrovirus

TaxID: 204507

Cluster

View cluster (45 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 66-237
PDB
Domain cluster: rep: MN698246.1__QGZ18180.1__HTVC112P_gp03__00003__D120-243
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3sm4A00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.82 62.0 5.56e-01 100.0% 58.7%
4ic1D00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.76 54.0 5.08e-01 100.0% 60.7%
1i74A02 3.10.310.20 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › DHHA2 domain 0.71 34.0 4.06e-01 91.9% 66.4%
2vldA02 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.69 41.0 5.05e-01 92.4% 91.7%
6ll8A02 3.10.310.20 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › DHHA2 domain 0.67 32.0 3.87e-01 91.3% 66.7%
2qb7B02 3.10.310.20 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › DHHA2 domain 0.64 33.0 3.62e-01 91.9% 60.7%
4hlbA00 3.30.70.2960 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 33.0 4.47e-01 70.3% 97.9%
4xqkA01 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.61 38.0 4.15e-01 90.7% 74.3%
4oa3A00 3.10.310.50 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › 0.61 31.0 3.35e-01 90.1% 56.0%
4dapA02 3.40.1350.60 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.59 43.0 4.53e-01 89.5% 84.2%
4qbnA00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.59 33.0 4.22e-01 87.2% 98.9%
3h4rA00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.58 53.0 4.85e-01 100.0% 76.3%
5zyuA01 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.58 54.0 5.16e-01 100.0% 91.5%
1tuoA02 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.56 27.0 3.53e-01 89.5% 85.9%
4hjhA02 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.55 27.0 3.60e-01 90.7% 91.4%
2dk6A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.52 22.0 2.87e-01 76.2% 68.1%
1u0mA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.51 34.0 3.63e-01 90.7% 78.8%
2dirA01 3.30.2300.10 Alpha Beta › 2-Layer Sandwich › THUMP fold › THUMP superfamily 0.50 26.0 3.54e-01 84.3% 98.9%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3614372 2008.1.1.50 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › YqaJ 0.80 60.0 5.15e-01 100.0% 51.2%
4933945 2008.1.1.4 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Cas_Cas4 0.78 57.0 5.28e-01 100.0% 60.0%
222168 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.76 54.0 5.08e-01 100.0% 60.7%
4314348 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.75 56.0 5.45e-01 100.0% 70.0%
4955488 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.74 47.0 5.85e-01 97.7% 100.0%
3945875 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.73 51.0 5.61e-01 89.0% 86.4%
5012280 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.71 55.0 5.16e-01 100.0% 66.3%
3606648 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.70 39.0 4.58e-01 89.5% 76.7%
5033908 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.70 59.0 5.52e-01 99.4% 73.2%
5000157 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.70 49.0 4.65e-01 100.0% 61.5%
5069954 2008.1.1.3 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Hjc 0.69 38.0 4.45e-01 86.6% 76.3%
4307642 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.69 41.0 5.07e-01 91.9% 95.2%
3249181 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.69 37.0 4.97e-01 84.9% 100.0%
4060516 2008.1.1.6 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › UPF0102 0.67 45.0 5.35e-01 91.3% 100.0%
5022195 2008.1.1.114 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF4143 0.67 35.0 4.65e-01 89.0% 94.4%
4954702 2008.1.1.114 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF4143 0.67 35.0 4.11e-01 88.4% 71.7%
5025921 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.66 38.0 4.68e-01 79.7% 89.1%
5063787 2008.1.1.5 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NucS_C 0.64 39.0 4.56e-01 90.1% 83.2%
5005253 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.64 43.0 4.44e-01 85.5% 71.9%
3822590 2008.1.1.77 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NOV_C 0.64 41.0 4.84e-01 91.9% 94.8%
3976411 2008.1.1.58 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF3799 0.64 60.0 5.18e-01 100.0% 75.6%
3580762 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.64 44.0 3.87e-01 100.0% 46.9%
3976034 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.63 35.0 4.22e-01 87.8% 80.0%
4290285 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.63 56.0 4.90e-01 99.4% 65.3%
4991881 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.63 40.0 4.92e-01 83.7% 99.1%
3992384 2008.1.1.29 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Dna2 0.63 60.0 5.45e-01 100.0% 85.9%
2715553 2008.1.1.34 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Card1_endonuc 0.63 41.0 4.80e-01 89.0% 93.3%
4942551 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.62 56.0 5.16e-01 100.0% 75.0%
4938605 2008.1.1.4 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Cas_Cas4 0.62 58.0 5.19e-01 100.0% 78.7%
4993521 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 40.0 4.69e-01 89.0% 93.3%
4247735 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.61 57.0 3.59e-01 99.4% 58.1%
4960194 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.60 56.0 4.78e-01 100.0% 74.3%
4927000 2008.1.1.217 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › UvrD-helicase 0.59 55.0 3.32e-01 100.0% 17.4%
4324924 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 51.0 5.19e-01 91.3% 94.5%
3726411 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 42.0 4.08e-01 91.9% 66.3%
5078654 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 38.0 4.53e-01 82.6% 95.0%
3839909 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.58 54.0 4.69e-01 100.0% 76.0%
3751785 3535.1.1.2 ↗ a+b two layers › Sex pheromone staph-cAM373 › Sex pheromone staph-cAM373 › Sex pheromone staph-cAM373 › SLFN_GTPase-like 0.58 43.0 4.56e-01 89.0% 84.5%
5005260 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.58 54.0 4.67e-01 100.0% 71.9%
3253903 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.58 54.0 4.98e-01 100.0% 90.5%
4962085 2008.1.1.11 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › SfsA 0.57 42.0 4.41e-01 90.1% 83.2%
4990214 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 52.0 5.05e-01 100.0% 87.9%
4950791 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.57 50.0 4.99e-01 95.9% 90.3%
3944117 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 39.0 4.06e-01 95.9% 74.1%
4990485 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.56 45.0 4.55e-01 93.6% 83.4%
4352045 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.56 25.0 3.20e-01 87.2% 72.2%
3555330 2008.1.1.97 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Exo5 0.56 52.0 4.35e-01 100.0% 77.5%
2439587 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.55 52.0 4.66e-01 100.0% 78.5%
5041197 2008.1.1.30 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Tn7_TnsA-like_N 0.54 34.0 3.48e-01 86.0% 62.4%
3617935 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.54 33.0 3.35e-01 70.3% 60.9%
4962258 2008.1.1.219 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF790 0.54 36.0 4.25e-01 84.9% 100.0%
5028573 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.53 40.0 4.44e-01 86.0% 96.4%
3206409 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.53 39.0 4.01e-01 91.9% 80.0%
3479948 2008.1.1.91 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NARG2_C 0.52 44.0 3.71e-01 100.0% 54.7%
4634054 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.52 37.0 4.23e-01 85.5% 98.4%
3734989 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.52 47.0 4.16e-01 98.3% 75.6%
4964258 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.51 37.0 3.97e-01 91.3% 87.6%
3499164 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.50 45.0 3.64e-01 100.0% 52.6%
3278307 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.50 33.0 3.62e-01 87.2% 78.6%
D2 high residues 246-312
PDB
Domain cluster: rep: alkaline_exonuclease__YP_010086987__Cryptophlebia_peltastica_nucleopolyhedrovirus__2304025__D258-315
D3 high residues 338-402
PDB
Domain cluster: rep: alkaline_exonuclease__YP_009117034__Pseudoplusia_includens_SNPV_IE__1592335__D351-412
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1i3oF00 1.10.1170.10 Mainly Alpha › Orthogonal Bundle › Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A › Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A 0.79 69.0 6.05e-01 93.8% 73.1%
5vmzA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.60 36.0 4.30e-01 84.6% 100.0%
1fumA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 38.0 2.51e-01 75.4% 76.1%
1ekgA00 3.30.920.10 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Frataxin/CyaY 0.51 35.0 2.94e-01 72.3% 94.1%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3492215 381.1.1.1 ↗ few secondary structure elements › Inhibitor of apoptosis (IAP) repeat › Inhibitor of apoptosis (IAP) repeat › Inhibitor of apoptosis (IAP) repeat › BIR 0.77 70.0 6.00e-01 98.5% 78.6%
3931141 381.1.1.0 ↗ few secondary structure elements › Inhibitor of apoptosis (IAP) repeat › Inhibitor of apoptosis (IAP) repeat › Inhibitor of apoptosis (IAP) repeat 0.71 58.0 6.19e-01 87.7% 98.3%
3903603 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.63 47.0 4.55e-01 81.5% 74.7%
3421203 386.1.1.20 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-met 0.58 45.0 4.64e-01 86.2% 100.0%
3274789 376.1.6.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › IBR domain 0.50 31.0 3.30e-01 80.0% 72.7%
D4 medium residues 1-65
PDB
Domain cluster: rep: alk-exo__YP_025138__Neodiprion_sertifer_nucleopolyhedrovirus__111874__D1-60