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glycoprotein

Euk-Vir

Cacao_swollen_shoot_Togo_A_virus

glycoprotein__YP_009506260__Cacao_swollen_shoot_Togo_A_virus__1960254

Identity

Accession:
YP_009506260 ↗
Protein ID:
glycoprotein
Kingdom:
euk

Quality

64.2 mean pLDDT

Taxonomy

Pararnavirae› Artverviricota› Revtraviricetes› Ortervirales› Caulimoviridae› Badnavirus› Cacao_swollen_shoot_Togo_A_virus

TaxID: 1960254

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 64-183
PDB
Domain cluster: rep: putative_glycoprotein__YP_002905332__Nyavirus_midwayense__644609__D72-196
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4f0aB02 3.30.2460.20 Alpha Beta › 2-Layer Sandwich › Endo-n-acetylneuraminidase fold › Wnt (Wingless and Int-1), C-terminal domain 0.72 26.0 3.45e-01 71.7% 57.4%
4r8tB02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.62 26.0 3.30e-01 100.0% 63.0%
4njcA00 3.10.20.730 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNAP, epsilon subunit-like 0.59 26.0 3.45e-01 100.0% 76.7%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.56 29.0 3.11e-01 70.8% 54.6%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 24.0 3.07e-01 100.0% 71.6%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1503409 220.3.1.1 ↗ beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Rhabdo_glycop 0.73 65.0 6.34e-01 100.0% 87.9%
1688016 220.3.1.3 ↗ beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Glycoprot_B_PH1 0.71 65.0 5.41e-01 100.0% 92.8%
3583154 220.3.1.0 ↗ beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins 0.70 64.0 6.06e-01 100.0% 90.7%
2530507 220.3.1.3 ↗ beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Glycoprot_B_PH1 0.68 63.0 5.08e-01 100.0% 88.3%
2124201 220.3.1.2 ↗ beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Baculo_gp64 0.62 55.0 5.09e-01 100.0% 96.8%
185186 220.3.1.2 ↗ beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Baculo_gp64 0.61 54.0 4.98e-01 100.0% 97.5%
2124211 220.3.1.2 ↗ beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Baculo_gp64 0.59 52.0 4.81e-01 100.0% 95.6%
2464208 220.3.1.2 ↗ beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Baculo_gp64 0.57 51.0 4.66e-01 100.0% 95.0%
3197303 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.56 39.0 3.12e-01 71.7% 62.2%
3737793 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.56 39.0 3.37e-01 71.7% 57.8%
3697761 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.56 39.0 3.11e-01 71.7% 64.0%
3192002 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.54 37.0 3.15e-01 71.7% 59.0%
3927415 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 32.0 3.44e-01 95.0% 69.2%
3898147 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.52 33.0 3.04e-01 71.7% 49.7%
3975660 5084.1.1.10 ↗ beta barrels › Outer membrane meander beta-barrels › OMPA-like › OMPA-like › OMP_b-brl 0.51 43.0 3.71e-01 99.2% 97.2%
D2 medium residues 37-59_197-249
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3fvcA03 2.30.29.100 Mainly Beta › Roll › PH-domain like › 0.75 60.0 5.32e-01 86.8% 94.5%
2cocA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 53.0 4.88e-01 85.5% 82.0%
3h8zA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.68 41.0 4.49e-01 85.5% 73.4%
1h10A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.66 52.0 4.64e-01 89.5% 79.5%
2d9xA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.66 51.0 4.57e-01 85.5% 72.7%
4c5eC02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.65 43.0 3.96e-01 85.5% 53.1%
1wi1A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.65 51.0 4.55e-01 86.8% 82.0%
4k17B01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.64 55.0 4.96e-01 100.0% 80.2%
2i2lB02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.64 42.0 4.38e-01 84.2% 75.0%
1bakA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 49.0 4.34e-01 86.8% 68.9%
1w1hD00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 54.0 4.56e-01 100.0% 59.9%
4hdoA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 49.0 4.69e-01 88.2% 81.5%
3lkmA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.61 48.0 3.83e-01 85.5% 87.3%
2codA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 46.0 4.36e-01 84.2% 82.3%
4tkoB01 2.40.30.170 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain 0.61 42.0 3.92e-01 85.5% 58.7%
4fw1A02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.60 40.0 4.50e-01 89.5% 96.3%
7mhwA01 2.40.128.10 Mainly Beta › Beta Barrel › Lipocalin › 0.60 46.0 4.44e-01 84.2% 95.5%
2k2jA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 46.0 4.08e-01 86.8% 76.1%
2yrvA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.58 42.0 3.66e-01 85.5% 50.4%
1ib8A02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.58 40.0 4.21e-01 85.5% 82.1%
1njhA00 2.70.180.10 Mainly Beta › Distorted Sandwich › Protein Yojf; Chain: A; › Hypothetical protein YojF 0.56 40.0 3.70e-01 78.9% 84.3%
2la7A01 2.40.128.270 Mainly Beta › Beta Barrel › Lipocalin › 0.55 42.0 3.61e-01 82.9% 91.4%
2krsA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.55 36.0 3.91e-01 84.2% 86.7%
1xkiA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 40.0 3.46e-01 80.3% 53.1%
3nbxX04 2.40.128.430 Mainly Beta › Beta Barrel › Lipocalin › 0.54 40.0 3.66e-01 82.9% 71.0%
6vp6A03 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 42.0 2.85e-01 90.8% 29.8%
2jkgA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.52 42.0 3.39e-01 94.7% 80.6%
2f5tX02 2.30.30.690 Mainly Beta › Roll › SH3 type barrels. › 0.51 38.0 3.71e-01 86.8% 72.2%
3oe3C00 2.40.128.200 Mainly Beta › Beta Barrel › Lipocalin › C-type lysozyme inhibitor 0.51 38.0 3.71e-01 84.2% 98.9%
1yemB00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.50 42.0 3.32e-01 94.7% 90.4%
ECOD (54)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3581696 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.75 47.0 5.59e-01 85.5% 96.0%
3570527 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.70 62.0 5.22e-01 100.0% 74.6%
3517079 220.1.1.47 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_16 0.70 61.0 5.02e-01 100.0% 89.0%
3262550 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.70 61.0 5.32e-01 100.0% 84.2%
3771814 220.1.1.47 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_16 0.70 61.0 4.64e-01 100.0% 61.1%
3173029 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.69 61.0 4.58e-01 100.0% 52.1%
3798262 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.69 60.0 4.89e-01 100.0% 82.0%
3263774 220.1.1.121 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_SLA1 0.69 61.0 4.84e-01 100.0% 56.8%
3937948 220.1.1.47 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_16 0.69 60.0 4.82e-01 100.0% 80.6%
3259097 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.69 60.0 5.14e-01 100.0% 72.8%
3266727 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.69 57.0 5.04e-01 93.4% 79.1%
3407061 220.1.1.47 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_16 0.68 60.0 4.88e-01 100.0% 80.7%
3620554 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.68 46.0 4.28e-01 85.5% 55.8%
3275009 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.68 59.0 4.85e-01 100.0% 68.5%
3536818 220.1.1.49 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Carm_PH 0.67 58.0 5.01e-01 100.0% 65.6%
3489980 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 56.0 4.79e-01 94.7% 83.2%
3743890 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 58.0 4.76e-01 100.0% 62.8%
3484357 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.66 57.0 5.07e-01 97.4% 84.5%
3556135 220.1.1.49 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Carm_PH 0.66 57.0 4.63e-01 100.0% 59.3%
3891866 220.1.1.49 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Carm_PH 0.65 55.0 4.62e-01 100.0% 60.7%
3914585 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.64 56.0 5.08e-01 100.0% 84.8%
3544563 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 55.0 5.05e-01 100.0% 84.8%
3473111 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.64 50.0 3.09e-01 86.8% 20.0%
3473704 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 50.0 4.81e-01 85.5% 87.1%
3929881 220.1.1.61 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C_FAK1 0.63 48.0 4.27e-01 84.2% 71.3%
3255034 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 53.0 4.53e-01 100.0% 65.2%
3936037 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.62 48.0 4.62e-01 85.5% 84.4%
4050317 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.62 53.0 4.61e-01 100.0% 80.0%
3722216 220.1.1.70 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_5 0.62 54.0 4.34e-01 100.0% 86.5%
3490300 243.4.1.6 ↗ a+b two layers › Cystatin-like › DsbC/DsbG N-terminal domain-like › DsbC/DsbG N-terminal domain-like › Radial_spoke 0.62 53.0 4.03e-01 100.0% 82.8%
3594856 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 48.0 4.31e-01 86.8% 75.5%
3921576 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 54.0 4.44e-01 100.0% 71.4%
4011604 4.1.1.13 ↗ beta barrels › SH3 › SH3 › SH3 › MS_channel_2nd 0.61 41.0 4.18e-01 84.2% 70.7%
3175712 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 47.0 3.72e-01 85.5% 55.2%
3574630 220.1.1.161 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF26659 0.60 46.0 4.01e-01 86.8% 61.5%
3971461 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.60 44.0 4.13e-01 85.5% 64.4%
3767975 220.1.1.38 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › UCH_N 0.60 45.0 4.06e-01 82.9% 72.7%
4093535 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.59 50.0 4.33e-01 100.0% 65.4%
1391581 4.1.1.34 ↗ beta barrels › SH3 › SH3 › SH3 › MBT 0.58 38.0 3.64e-01 86.8% 54.8%
3579992 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.58 49.0 4.04e-01 100.0% 61.3%
3703442 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 50.0 4.90e-01 98.7% 88.2%
3761318 4.1.1.253 ↗ beta barrels › SH3 › SH3 › SH3 › DUF4537 0.55 40.0 4.15e-01 85.5% 82.9%
3336357 3794.1.1.4 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › MCCA_BT 0.54 40.0 3.24e-01 81.6% 58.2%
4130525 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.54 44.0 2.77e-01 90.8% 24.7%
3974575 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.54 43.0 3.97e-01 85.5% 71.4%
3636368 3794.1.1.0 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit 0.54 42.0 3.51e-01 86.8% 70.7%
4075020 1.1.7.88 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25963 0.53 43.0 3.47e-01 85.5% 55.8%
4284005 868.1.1.3 ↗ a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › Med20 0.53 43.0 3.34e-01 93.4% 92.7%
4050380 1.1.7.95 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25990 0.53 43.0 3.97e-01 85.5% 72.6%
3599152 3794.1.1.0 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit 0.53 41.0 3.42e-01 85.5% 63.6%
3316055 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.50 42.0 3.04e-01 100.0% 75.3%
3250470 3307.1.1.0 ↗ a+b two layers › Domain in small RNA methyltransferase HEN1 › Domain in small RNA methyltransferase HEN1 › Domain in small RNA methyltransferase HEN1 0.50 39.0 3.79e-01 86.8% 96.7%
3736175 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.50 43.0 4.22e-01 97.4% 88.2%
3035660 3794.1.1.1 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › PCC_BT 0.50 38.0 3.24e-01 84.2% 78.5%