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GrBNV_gp28-like_protein

Euk-Vir

Oryctes_rhinoceros_nudivirus

GrBNV_gp28-like_protein__YP_002321401__Oryctes_rhinoceros_nudivirus__92521

Identity

Accession:
YP_002321401 ↗
Protein ID:
GrBNV_gp28-like_protein
Kingdom:
euk

Quality

47.2 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Nudiviridae› Alphanudivirus› Oryctes_rhinoceros_nudivirus

TaxID: 92521

Cluster

View cluster (2 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 612-782
PDB
D2 medium residues 344-486_575-611
PDB
D3 medium residues 487-574
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u89A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.74 64.0 5.51e-01 95.5% 80.6%
2lseA00 1.20.120.1360 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.72 64.0 6.11e-01 96.6% 89.1%
3jsbA01 1.20.1440.300 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain 0.67 55.0 5.68e-01 92.0% 96.3%
1kz7A01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.66 56.0 4.43e-01 95.5% 90.2%
1orjD00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.66 48.0 4.26e-01 76.1% 71.2%
5u56A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.65 49.0 4.50e-01 79.5% 75.9%
1iurA01 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.64 41.0 4.72e-01 83.0% 92.1%
2qwoB00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.62 51.0 5.07e-01 89.8% 84.8%
7p5hB03 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.62 50.0 5.06e-01 88.6% 94.4%
7vkcA01 1.10.1070.20 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › 0.61 52.0 4.15e-01 90.9% 90.9%
3k2jA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.60 50.0 4.53e-01 92.0% 86.0%
5xfaA04 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.60 47.0 4.85e-01 87.5% 97.6%
4fqnC00 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.60 50.0 5.15e-01 94.3% 94.1%
1fewA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 43.0 3.50e-01 76.1% 69.4%
6q9jB02 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.60 48.0 4.88e-01 92.0% 89.8%
1mswD04 1.10.287.280 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 46.0 4.89e-01 94.3% 94.9%
2x64A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 44.0 4.08e-01 80.7% 74.3%
5fzsA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.58 36.0 3.42e-01 77.3% 50.5%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.57 48.0 4.12e-01 95.5% 64.5%
1v9vA01 1.20.1480.20 Mainly Alpha › Up-down Bundle › hypothetical protein mp506/mpn330, domain 1 › MAST3 pre-PK domain-like 0.57 47.0 4.66e-01 94.3% 98.9%
2h7oA01 1.20.120.1330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Rac1-binding domain, N-terminal GTPase binding subdomain 0.57 42.0 3.82e-01 78.4% 88.6%
1pmiA02 1.10.441.10 Mainly Alpha › Orthogonal Bundle › Phosphomannose Isomerase; domain 2 › Phosphomannose Isomerase, domain 2 0.57 46.0 4.05e-01 90.9% 91.9%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.56 41.0 4.34e-01 94.3% 92.0%
1wu3I00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.56 48.0 3.95e-01 95.5% 59.0%
6ljaA01 1.50.10.100 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Chondroitin AC/alginate lyase 0.55 49.0 3.29e-01 100.0% 39.7%
5cwkA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.55 42.0 3.44e-01 81.8% 46.4%
3mzoB00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.55 42.0 3.23e-01 81.8% 80.0%
4pxoA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 40.0 3.60e-01 78.4% 70.2%
2kiwA01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.55 45.0 4.61e-01 90.9% 93.0%
4jxtA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.54 44.0 3.89e-01 88.6% 77.7%
2a0uB01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.54 39.0 3.27e-01 77.3% 64.4%
3d2eA06 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.54 40.0 3.72e-01 78.4% 74.3%
2yx0A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.54 40.0 2.74e-01 78.4% 57.4%
6tblB01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.53 38.0 3.61e-01 77.3% 60.4%
3m0fB02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 39.0 3.51e-01 78.4% 74.0%
6vxcA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.52 46.0 2.71e-01 100.0% 52.9%
6wfqC01 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.52 47.0 3.98e-01 98.9% 70.4%
4dkcB00 1.20.1250.80 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › Interleukin-34 0.52 43.0 3.69e-01 96.6% 63.7%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 39.0 3.62e-01 80.7% 70.9%
4evfA02 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.52 37.0 3.92e-01 75.0% 95.9%
2icwG02 1.10.10.530 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › mam-mhc complex, Chain D, Domain 2 0.52 35.0 3.51e-01 84.1% 67.4%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.50 40.0 4.14e-01 90.9% 95.1%
8hk0A01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.50 37.0 3.44e-01 80.7% 91.6%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4543944 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.68 59.0 4.64e-01 95.5% 49.2%
4169956 604.12.1.26 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › HemX 0.68 45.0 4.85e-01 76.1% 80.0%
3244741 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.68 59.0 4.97e-01 97.7% 85.3%
5001312 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.67 56.0 5.85e-01 92.0% 100.0%
4080847 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.67 50.0 5.52e-01 86.4% 100.0%
4027904 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.66 57.0 5.32e-01 96.6% 95.5%
4976933 3930.1.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.65 48.0 4.23e-01 97.7% 51.9%
3664127 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 53.0 3.51e-01 95.5% 40.8%
3480264 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.62 54.0 5.28e-01 96.6% 89.5%
3940500 3198.1.1.0 ↗ alpha bundles › ABA-1 repeat unit › ABA-1 repeat unit › ABA-1 repeat unit 0.60 48.0 4.71e-01 85.2% 93.6%
3502686 2484.1.1.88 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ParM_N 0.59 41.0 3.39e-01 72.7% 73.3%
3500097 310.2.1.32 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › Oxidored-like 0.57 44.0 4.39e-01 80.7% 78.9%
3731006 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.57 41.0 4.04e-01 76.1% 89.5%
5052411 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.56 43.0 4.15e-01 80.7% 77.0%
3692194 6155.1.1.0 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.56 37.0 3.83e-01 95.5% 72.5%
135559 186.1.1.5 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_3 0.56 48.0 4.56e-01 94.3% 86.4%
3282529 632.1.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid 0.56 42.0 4.06e-01 84.1% 94.3%
3819682 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.55 34.0 3.64e-01 89.8% 72.0%
3341807 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.55 39.0 3.73e-01 75.0% 70.0%
3688545 109.1.1.36 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_N 0.55 45.0 3.31e-01 92.0% 84.7%
3435297 109.4.1.954 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_EF3_N 0.54 39.0 3.27e-01 77.3% 45.6%
3920960 604.8.1.2 ↗ alpha bundles › Spectrin repeat-like › Smac/diablo › Smac/diablo › Mitofilin 0.53 39.0 3.49e-01 78.4% 74.6%
5000955 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 0.52 43.0 3.37e-01 95.5% 78.6%
4583265 108.1.1.114 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_1, EF-hand_5, EF-hand_6, EF-hand_7 0.51 40.0 3.28e-01 89.8% 94.1%
3033368 4033.1.1.0 ↗ alpha arrays › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like 0.50 37.0 3.43e-01 79.5% 87.5%
D4 medium residues 906-957_974-997
PDB