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capsid_protein

Euk-Vir

Sporobolus_striate_mosaic_virus_1

capsid_protein__YP_006666526__Sporobolus_striate_mosaic_virus_1__1302849

Identity

Accession:
YP_006666526 ↗
Protein ID:
capsid_protein
Kingdom:
euk

Quality

87.3 mean pLDDT

Taxonomy

Shotokuvirae› Cressdnaviricota› Repensiviricetes› Geplafuvirales› Geminiviridae› Mastrevirus› Sporobolus_striate_mosaic_virus_1

TaxID: 1302849

Cluster

View cluster (551 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 medium residues 22-78_127-169_187-212
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6f2sH01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.85 80.0 6.47e-01 97.6% 80.5%
4bcuA00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.71 65.0 5.61e-01 97.6% 85.1%
3ks7A02 2.60.120.230 Mainly Beta › Sandwich › Jelly Rolls › 0.60 53.0 4.70e-01 95.2% 95.0%
4xuoA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.60 51.0 4.72e-01 96.0% 73.1%
4qpiB00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.60 54.0 4.52e-01 100.0% 70.0%
4lejA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.60 37.0 3.33e-01 96.8% 44.4%
6tfjA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.59 43.0 4.48e-01 93.7% 82.6%
3s7vC00 2.60.175.10 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus 0.59 52.0 4.11e-01 98.4% 91.8%
2hyxA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.58 36.0 3.59e-01 92.9% 58.8%
4yarA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 33.0 3.40e-01 93.7% 56.9%
1p8jA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.58 49.0 4.82e-01 96.0% 87.1%
2df7A02 2.60.120.660 Mainly Beta › Sandwich › Jelly Rolls › icosahedral virus 0.58 52.0 5.04e-01 96.8% 94.3%
4icwA00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.57 40.0 3.97e-01 71.4% 98.5%
1b35C00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.57 50.0 3.91e-01 98.4% 65.2%
4zrxA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.56 40.0 4.33e-01 95.2% 87.6%
6eiwA01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.56 51.0 4.43e-01 100.0% 92.7%
4ozxA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.56 49.0 3.76e-01 95.2% 81.4%
4kq7A02 2.60.120.1390 Mainly Beta › Sandwich › Jelly Rolls › Protein of unknown function DUF2961 0.56 50.0 4.19e-01 96.8% 73.0%
1alyA00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.56 49.0 4.66e-01 94.4% 91.8%
1a6cA02 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.56 49.0 4.54e-01 98.4% 90.3%
7u7nA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 34.0 3.80e-01 98.4% 78.4%
1o5uA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.55 31.0 3.54e-01 92.1% 75.0%
1b35A00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.55 50.0 3.92e-01 98.4% 72.7%
1a8mA00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.55 48.0 4.57e-01 96.0% 90.8%
4ag4A02 2.60.120.1190 Mainly Beta › Sandwich › Jelly Rolls › 0.55 46.0 4.09e-01 96.8% 63.0%
2nq3A00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.55 40.0 3.95e-01 75.4% 100.0%
1mec100 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.54 47.0 3.73e-01 97.6% 75.5%
2fmyA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.54 27.0 2.66e-01 94.4% 41.9%
1lnsA04 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 47.0 4.13e-01 96.0% 83.3%
4mloA01 2.60.120.810 Mainly Beta › Sandwich › Jelly Rolls › 0.53 33.0 3.10e-01 94.4% 48.4%
4jdmA03 2.60.120.1340 Mainly Beta › Sandwich › Jelly Rolls › 0.53 46.0 4.32e-01 95.2% 87.7%
2q1fA01 2.60.120.430 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding lectin 0.52 44.0 3.98e-01 95.2% 67.7%
1dhkB00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 46.0 3.97e-01 95.2% 94.9%
7chkB01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.52 45.0 4.51e-01 96.8% 96.2%
4nhxA01 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.52 39.0 3.28e-01 97.6% 45.9%
4ht1T00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.51 45.0 4.48e-01 96.0% 93.9%
3bb6C00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.51 35.0 3.70e-01 92.9% 78.6%
2waaA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 41.0 4.20e-01 95.2% 88.6%
1mpxA03 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 44.0 3.62e-01 96.8% 82.8%
4jqtA01 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.50 44.0 3.78e-01 95.2% 79.6%
1w99A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.50 43.0 3.78e-01 95.2% 78.5%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3108819 10.2.1.11 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Gemini_coat 0.88 84.0 6.77e-01 99.2% 88.8%
2841541 10.2.1.11 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Gemini_coat 0.84 81.0 6.53e-01 100.0% 80.7%
4058249 10.34.1.1 ↗ beta sandwiches › jelly-roll › Protein CLP1 jelly-roll domain › Protein CLP1 jelly-roll domain › CLP1_N 0.66 35.0 4.47e-01 93.7% 91.4%
3259597 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.65 51.0 4.57e-01 96.8% 60.6%
3266593 11.2.1.17 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › NT-C2 0.61 45.0 4.08e-01 77.0% 82.4%
5005697 10.34.1.0 ↗ beta sandwiches › jelly-roll › Protein CLP1 jelly-roll domain › Protein CLP1 jelly-roll domain 0.60 28.0 3.74e-01 92.1% 86.7%
3222807 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.60 47.0 4.88e-01 93.7% 89.6%
3889245 11.2.1.7 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › Anillin 0.60 43.0 3.46e-01 75.4% 65.7%
3291768 11.2.1.17 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › NT-C2 0.59 44.0 4.07e-01 77.0% 98.1%
3347639 11.2.1.17 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › NT-C2 0.57 41.0 4.01e-01 73.0% 99.3%
4667107 10.3.1.0 ↗ beta sandwiches › jelly-roll › TNF-like › TNF-like 0.57 51.0 4.90e-01 97.6% 93.8%
3809848 10.32.1.199 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DUF642 0.57 47.0 4.28e-01 95.2% 65.9%
3415782 10.32.1.172 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DDR1-2_DS-like 0.57 49.0 4.28e-01 99.2% 63.2%
5033996 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.57 50.0 4.03e-01 96.8% 84.5%
2710690 10.2.1.29 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Circo_capsid 0.56 50.0 4.29e-01 97.6% 86.6%
3928527 10.32.1.172 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DDR1-2_DS-like 0.56 47.0 4.17e-01 96.8% 62.8%
3583509 10.32.1.172 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DDR1-2_DS-like 0.56 47.0 4.18e-01 95.2% 64.6%
3882246 10.32.1.172 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DDR1-2_DS-like 0.56 47.0 4.08e-01 97.6% 59.0%
3935284 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.56 40.0 3.50e-01 74.6% 86.8%
3545336 10.3.1.1 ↗ beta sandwiches › jelly-roll › TNF-like › TNF-like › TNF 0.55 48.0 4.52e-01 95.2% 89.0%
4491474 10.32.1.31 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › PepX_C 0.55 48.0 4.27e-01 95.2% 82.8%
3927919 11.2.1.20 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › FerB 0.55 38.0 3.52e-01 72.2% 94.5%
3478145 10.32.1.172 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DDR1-2_DS-like 0.54 48.0 4.16e-01 96.8% 62.4%
3458852 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.54 48.0 4.33e-01 95.2% 95.9%
3490271 10.32.1.172 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DDR1-2_DS-like 0.54 46.0 4.08e-01 96.0% 63.0%
3472554 10.32.1.6 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › P_proprotein 0.54 47.0 4.37e-01 98.4% 90.9%
4944752 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.53 46.0 4.71e-01 94.4% 97.5%
3741799 10.32.1.24 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › PITH 0.53 45.0 4.23e-01 96.8% 74.2%
3699775 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.53 48.0 4.68e-01 97.6% 93.3%
3580333 11.2.1.20 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › FerB 0.53 39.0 3.40e-01 76.2% 86.8%
3512330 10.32.1.176 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DUF3672 0.53 46.0 4.50e-01 95.2% 88.1%
3762739 10.4.1.1 ↗ beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain › CUB 0.52 37.0 3.84e-01 95.2% 77.5%
4857421 11.1.1.361 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Glyco_hydro_123_N_2 0.52 36.0 3.54e-01 71.4% 97.1%
1878989 10.2.1.29 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Circo_capsid 0.52 45.0 3.94e-01 100.0% 90.3%
2665487 10.2.1.103 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Vp24_capsid 0.52 45.0 4.36e-01 99.2% 88.4%
3345932 11.2.1.54 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › DUF1005 0.51 36.0 3.36e-01 71.4% 98.1%
3570861 10.1.1.17 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.51 45.0 3.71e-01 94.4% 82.3%
3924218 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.51 28.0 2.97e-01 95.2% 57.4%
1156538 10.32.1.56 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › CE2_N 0.51 41.0 4.20e-01 95.2% 88.6%
3802666 207.1.1.133 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1, LRR_14 0.51 41.0 2.79e-01 88.1% 24.2%
D2 medium residues 79-126_170-186
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00844.25 best Gemini_coat 50.2 3.40e-13 78.5% 19.3%
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6f2sH01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.90 84.0 5.64e-01 100.0% 42.8%
2cpxA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.56 38.0 3.63e-01 72.3% 97.5%
3zzoA00 3.30.70.2800 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 37.0 3.34e-01 73.8% 84.9%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3108819 10.2.1.11 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Gemini_coat 0.95 90.0 6.00e-01 100.0% 50.7%
3458310 304.9.1.20 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_8 0.53 36.0 3.12e-01 73.8% 64.3%
3304434 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.50 35.0 3.45e-01 73.8% 87.1%