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endonuclease

Euk-Vir

Apocheima_cinerarium_nucleopolyhedrovirus

endonuclease__YP_006607843__Apocheima_cinerarium_nucleopolyhedrovirus__307461

Identity

Accession:
YP_006607843 ↗
Protein ID:
endonuclease
Kingdom:
euk

Quality

88.0 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Alphabaculovirus› Apocheima_cinerarium_nucleopolyhedrovirus

TaxID: 307461

Cluster

View cluster (28 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 8-91
PDB
Domain cluster: rep: H2c1_full_idba_ud_scaffold_88_prodigal-single.1__X__X__00452__D3-76
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01541.31 best GIY-YIG 48.4 1.40e-12 88.1% 94.9%
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.83 64.0 6.26e-01 82.1% 87.0%
4gr5C01 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.74 40.0 4.56e-01 79.8% 70.3%
5ja1B00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.72 39.0 4.40e-01 79.8% 68.2%
2pstX00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.69 40.0 4.68e-01 82.1% 80.3%
1qr4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 37.0 3.73e-01 100.0% 52.9%
1ywlA00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.66 59.0 5.63e-01 98.8% 88.5%
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.65 35.0 4.09e-01 77.4% 75.4%
1mgpA01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.64 52.0 4.31e-01 90.5% 100.0%
2yn5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 34.0 3.58e-01 98.8% 57.0%
3nyiB01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.60 48.0 4.01e-01 90.5% 100.0%
3hu1A01 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.59 37.0 3.52e-01 97.6% 55.2%
2qsdB02 3.50.100.10 Alpha Beta › 3-Layer(bba) Sandwich › protein il1583 fold › protein il1583 domain 0.57 38.0 3.98e-01 79.8% 75.6%
2nutB01 1.20.120.730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sec23/Sec24 helical domain 0.55 42.0 3.49e-01 83.3% 66.0%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.54 37.0 3.59e-01 100.0% 62.5%
7p0eA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 33.0 3.17e-01 91.7% 52.5%
1o54A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.52 35.0 3.80e-01 89.3% 80.6%
1u3eM02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.51 32.0 3.58e-01 98.8% 79.4%
4limA00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.50 39.0 2.60e-01 86.9% 76.9%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3942510 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.97 93.0 8.83e-01 100.0% 87.4%
4158495 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.93 89.0 8.65e-01 100.0% 95.6%
4997210 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.92 82.0 8.03e-01 97.6% 87.8%
4397568 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.91 87.0 8.49e-01 100.0% 94.4%
3971569 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.91 81.0 8.08e-01 94.0% 91.8%
4557537 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.91 81.0 7.88e-01 94.0% 86.7%
4623707 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.91 86.0 8.23e-01 100.0% 91.6%
4669741 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.90 81.0 7.71e-01 98.8% 83.2%
3965455 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.85 76.0 7.39e-01 94.0% 87.8%
5046850 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.85 74.0 7.20e-01 92.9% 86.7%
3738592 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.81 75.0 5.92e-01 100.0% 82.4%
3400250 379.1.1.3 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors › Kazal_2 0.73 37.0 4.64e-01 85.7% 82.0%
5049794 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.68 46.0 3.80e-01 100.0% 40.0%
4969863 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.68 46.0 4.88e-01 70.2% 82.7%
5001166 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.67 43.0 3.70e-01 100.0% 40.7%
1003912 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.66 59.0 5.63e-01 98.8% 88.5%
1844216 4007.1.1.1 ↗ a+b two layers › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › Transcrip_reg 0.66 38.0 4.67e-01 86.9% 94.1%
5747 4007.1.1.1 ↗ a+b two layers › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › Transcrip_reg 0.63 38.0 4.64e-01 88.1% 94.4%
4004704 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.63 35.0 4.30e-01 98.8% 100.0%
5061599 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 37.0 3.69e-01 92.9% 60.0%
3987692 822.3.1.1 ↗ a+b two layers › GYF/BRK domain-like › conserved domain protein SP_1775 › conserved domain protein SP_1775 › DUF4649 0.59 35.0 3.83e-01 91.7% 71.4%
3907337 4076.2.1.0 ↗ a+b two layers › L9 N-domain-like › MbtH-like › MbtH-like 0.57 46.0 4.50e-01 85.7% 95.6%
4988123 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 35.0 3.18e-01 90.5% 46.1%
3811678 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.56 43.0 3.94e-01 100.0% 63.0%
3344184 11.1.1.652 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ribophorin_II_3rd 0.56 39.0 3.29e-01 91.7% 42.8%
1217180 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.55 42.0 2.91e-01 83.3% 75.2%
3975440 10.12.1.85 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_6 0.54 46.0 3.74e-01 100.0% 64.0%
4025385 2003.1.5.82 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.52 36.0 2.86e-01 72.6% 71.1%
3930427 4357.1.1.0 ↗ beta barrels › WWE domain › WWE domain › WWE domain 0.51 33.0 3.65e-01 90.5% 84.6%