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p28

Euk-Vir

Diodia_vein_chlorosis_virus

p28__YP_009507959__Diodia_vein_chlorosis_virus__656520

Identity

Accession:
YP_009507959 ↗
Protein ID:
p28
Kingdom:
euk

Quality

78.6 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Martellivirales› Closteroviridae› Crinivirus› Diodia_vein_chlorosis_virus

TaxID: 656520

Cluster

View cluster (11 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 20-131
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4a17U01 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.79 44.0 5.32e-01 85.7% 81.8%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.79 45.0 4.65e-01 75.9% 60.4%
4hwdD00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.68 51.0 5.60e-01 98.2% 95.6%
3ejnA01 1.25.40.390 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.68 57.0 4.61e-01 98.2% 50.3%
2qgmA03 1.20.1440.30 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Biosynthetic Protein domain 0.65 43.0 4.32e-01 98.2% 65.5%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 47.0 3.98e-01 100.0% 45.7%
2a3qA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.65 39.0 3.91e-01 79.5% 60.2%
1vdyA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.64 38.0 3.54e-01 96.4% 45.7%
3whjA00 6.10.140.1710 Special › Helix non-globular › Helix Hairpins › 0.63 46.0 4.67e-01 92.9% 76.6%
7fhyB01 1.50.10.100 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Chondroitin AC/alginate lyase 0.62 43.0 3.18e-01 93.8% 27.5%
3f2kB00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.61 45.0 3.79e-01 75.9% 99.5%
2p61A00 1.20.120.490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hypothetical protein TM1646-like domain 0.61 43.0 4.35e-01 100.0% 71.9%
5y06A01 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 44.0 3.53e-01 77.7% 99.1%
1wn0A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.60 39.0 3.71e-01 97.3% 55.7%
2yk0A03 1.20.58.1930 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 53.0 4.23e-01 100.0% 64.8%
3wd6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 45.0 4.41e-01 98.2% 75.4%
6wv5A01 1.20.1440.130 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › VKOR domain 0.58 48.0 4.48e-01 99.1% 72.8%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.57 44.0 4.17e-01 99.1% 67.9%
6t0bc02 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.57 48.0 3.97e-01 98.2% 52.4%
2hz8A00 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.57 42.0 4.25e-01 97.3% 77.4%
2qupA00 1.20.120.490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hypothetical protein TM1646-like domain 0.56 41.0 4.10e-01 100.0% 73.9%
1rfyB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.55 39.0 4.34e-01 81.2% 92.0%
2ntxA01 1.20.58.2010 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › PRONE domain, subdomain 1 0.54 50.0 3.99e-01 100.0% 53.3%
5j1hA01 1.20.58.1060 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 49.0 4.14e-01 100.0% 85.7%
2cz2A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.54 40.0 3.87e-01 94.6% 69.8%
6vq6G02 1.20.1460.10 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › subunit c (vma5p) of the yeast v-atpase, domain 2 0.52 41.0 3.43e-01 82.1% 98.4%
5dqqA01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.51 41.0 3.99e-01 98.2% 76.6%
6tqpA01 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.50 33.0 3.18e-01 98.2% 54.4%
1jqjC02 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.50 39.0 4.18e-01 88.4% 94.8%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5046472 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.72 56.0 6.01e-01 100.0% 94.7%
3595289 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.69 46.0 4.93e-01 96.4% 78.9%
5084013 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.67 50.0 5.09e-01 99.1% 80.0%
3333216 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.67 50.0 5.45e-01 99.1% 92.6%
3430123 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.67 44.0 3.78e-01 96.4% 42.2%
3970945 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.63 47.0 4.66e-01 93.8% 75.7%
3934833 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.62 45.0 4.87e-01 98.2% 90.5%
3510890 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.61 46.0 4.52e-01 99.1% 73.3%
3553783 109.4.1.1660 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF27570 0.61 48.0 3.66e-01 100.0% 36.5%
5072346 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.61 54.0 4.47e-01 96.4% 85.5%
3255241 601.1.2.6 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Talin_IBS2B 0.61 42.0 4.25e-01 95.5% 70.4%
3398541 109.4.1.1492 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_SCC3-SA, PF31007 0.61 43.0 2.84e-01 92.9% 18.6%
3577736 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.60 45.0 4.48e-01 99.1% 74.2%
3727312 192.2.1.6 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_3 0.60 44.0 4.52e-01 75.9% 77.3%
3274541 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.59 50.0 4.75e-01 100.0% 78.5%
3980942 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.58 35.0 3.77e-01 83.0% 69.0%
3561226 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.58 39.0 3.90e-01 93.8% 65.8%
3735108 3711.1.1.0 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein 0.57 36.0 3.19e-01 80.4% 45.2%
3934654 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.57 53.0 4.44e-01 99.1% 63.3%
3546316 3922.1.1.186 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › WWC1 0.57 39.0 3.34e-01 70.5% 87.0%
3352030 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 51.0 3.40e-01 100.0% 25.6%
3499418 5057.1.1.0 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.57 42.0 4.01e-01 99.1% 65.9%
3724963 109.4.1.528 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CBF 0.56 49.0 3.61e-01 97.3% 36.7%
3574330 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.55 31.0 3.15e-01 75.9% 53.9%
3938941 109.4.1.649 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF4807 0.55 51.0 4.83e-01 100.0% 88.5%
3804219 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.54 27.0 3.01e-01 81.2% 61.1%
3194774 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.54 49.0 3.75e-01 100.0% 53.8%
4999535 5057.1.1.0 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.54 42.0 4.37e-01 99.1% 89.5%
3490867 5069.1.1.1 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cytochrome_B 0.53 39.0 3.13e-01 76.8% 38.2%
3176998 633.23.1.12 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Fig1 0.53 48.0 3.81e-01 100.0% 50.0%
4935669 601.33.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain › CHAD 0.53 46.0 4.31e-01 100.0% 77.1%
3704526 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.53 48.0 4.20e-01 99.1% 83.6%
None — 0.52 48.0 4.27e-01 100.0% 88.4%
3171401 633.23.1.9 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 0.52 45.0 3.62e-01 100.0% 48.2%
3576275 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.52 47.0 4.51e-01 100.0% 86.9%
3206514 192.2.1.6 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_3 0.52 38.0 3.61e-01 75.9% 71.5%
3610578 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.52 45.0 4.18e-01 100.0% 75.2%
3826620 611.7.1.16 ↗ alpha bundles › N-cbl like › Mixed lineage kinase domain-like (MLKL) N-terminal domain › Mixed lineage kinase domain-like (MLKL) N-terminal domain › PUB2_N 0.52 37.0 3.49e-01 91.1% 60.0%
3602143 3755.3.1.305 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › Rad50_zn_hook 0.51 38.0 2.85e-01 75.9% 37.1%
4578350 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.51 36.0 2.93e-01 74.1% 68.4%
3617270 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.51 46.0 4.26e-01 100.0% 87.9%
D2 high residues 136-237
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d00A01 3.30.1330.130 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › 0.57 45.0 3.99e-01 87.3% 91.5%
2uvaG08 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.56 45.0 3.26e-01 86.3% 42.3%
5i97C00 3.10.450.230 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › VirB8 protein 0.55 45.0 4.04e-01 86.3% 100.0%
3b7kB01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.54 48.0 4.34e-01 100.0% 93.6%
3cjrB01 3.30.1550.10 Alpha Beta › 2-Layer Sandwich › Ribosomal protein L11, N-terminal domain › Ribosomal protein L11/L12, N-terminal domain 0.53 31.0 3.59e-01 80.4% 84.3%
1rniA01 3.30.720.160 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Bifunctional DNA primase/polymerase, N-terminal 0.52 30.0 3.52e-01 81.4% 82.9%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3929839 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 45.0 4.15e-01 92.2% 60.7%
4996310 325.1.2.1 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Molybdopterin synthase subunit MoaE › MoaE 0.55 44.0 3.97e-01 86.3% 99.3%
3933042 5.1.3.12 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Str_synth 0.53 45.0 3.18e-01 99.0% 81.4%
3545968 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 42.0 2.43e-01 88.2% 15.8%
4945422 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.50 34.0 2.68e-01 70.6% 93.6%
3831916 5.1.3.12 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Str_synth 0.50 42.0 3.06e-01 97.1% 95.4%