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VP2

Euk-Vir

Rotavirus_G_chicken_03V0567_DEU_2003

VP2__YP_008136231__Rotavirus_G_chicken_03V0567_DEU_2003__994995

Identity

Accession:
YP_008136231 ↗
Protein ID:
VP2
Kingdom:
euk

Quality

71.6 mean pLDDT

Cluster

View cluster (4 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 3-81
PDB
D2 medium residues 176-246
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25649.1 best Rotavirus_VP2 46.6 1.70e-12 100.0% 7.1%
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3gveA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.61 43.0 2.78e-01 74.6% 56.0%
2c4eA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.55 47.0 3.19e-01 100.0% 86.0%
4je5C00 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.54 38.0 2.38e-01 77.5% 64.2%
4f3lA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 33.0 2.87e-01 84.5% 38.3%
3bzwF00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.52 44.0 3.15e-01 100.0% 40.3%
3ie7A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 41.0 2.79e-01 93.0% 42.4%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3463916 1.1.1.20 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › TAXi_C+TAXi_N 0.52 36.0 2.40e-01 71.8% 18.2%
5000532 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.51 35.0 2.67e-01 73.2% 36.1%
369252 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.51 41.0 2.79e-01 93.0% 42.4%
D3 medium residues 247-334_947-959
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25649.1 best Rotavirus_VP2 94.3 6.70e-27 99.0% 9.0%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2589759 4064.1.1.2 ↗ a+b complex topology › Inner layer core protein p3-related › Inner layer core protein p3-related › Inner layer core protein p3-related › Rota_VP2 0.79 73.0 4.23e-01 100.0% 81.5%
4484798 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.56 34.0 3.56e-01 96.0% 64.2%
5006277 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.54 26.0 3.34e-01 95.0% 85.7%
3994712 3016.1.1.10 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › GDC-P 0.53 34.0 3.41e-01 97.0% 64.0%
4944732 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.53 29.0 3.48e-01 80.2% 81.5%
3724547 4317.1.1.1 ↗ a+b duplicates or obligate multimers › YdfO-like › YdfO-like › YdfO-like › DUF1398 0.52 27.0 3.37e-01 92.1% 81.7%
5049591 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.52 31.0 3.78e-01 80.2% 92.3%
5023789 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.51 32.0 3.48e-01 98.0% 75.3%
3290823 809.1.1.0 ↗ a+b two layers › BLIP-like › beta-lactamase-inhibitor protein, BLIP › beta-lactamase-inhibitor protein, BLIP 0.50 27.0 3.11e-01 98.0% 70.7%
D4 medium residues 335-394
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25649.1 best Rotavirus_VP2 60.1 1.40e-16 100.0% 5.9%
D5 medium residues 395-450
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25649.1 best Rotavirus_VP2 57.3 9.80e-16 100.0% 5.7%
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3of4A00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.57 43.0 3.03e-01 89.3% 23.2%
3hqiA02 3.30.710.10 Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A 0.55 39.0 2.98e-01 76.8% 59.3%
1zboA02 1.10.4060.10 Mainly Alpha › Orthogonal Bundle › LON domain-like fold › BPP1347 like domain 0.52 39.0 3.52e-01 85.7% 91.7%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4964983 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.64 54.0 4.71e-01 98.2% 71.1%
4322644 4967.1.1.0 ↗ alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.63 50.0 4.00e-01 91.1% 45.6%
5043976 3678.1.1.0 ↗ alpha arrays › Pilus-presented adhesin helical insertion domain › Pilus-presented adhesin helical insertion domain › Pilus-presented adhesin helical insertion domain 0.59 44.0 3.46e-01 80.4% 40.0%
3591186 7087.1.1.1 ↗ alpha bundles › Emopamil binding protein (EBP) transmembrane domain › Emopamil binding protein (EBP) transmembrane domain › Emopamil binding protein (EBP) transmembrane domain › EBP 0.59 44.0 3.34e-01 89.3% 90.3%
3659378 109.4.1.1273 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3 0.58 39.0 2.55e-01 80.4% 14.2%
3923243 864.1.1.3 ↗ a+b two layers › DLC › DLC › DLC › Ground-like 0.58 41.0 3.59e-01 75.0% 46.7%
5009433 5042.1.1.1 ↗ extended segments › Magnesium transport protein CorA, transmembrane region › Magnesium transport protein CorA, transmembrane region › Magnesium transport protein CorA, transmembrane region › CorA 0.58 45.0 4.37e-01 92.9% 87.7%
3219593 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.58 45.0 4.39e-01 89.3% 90.8%
3597523 5076.1.1.0 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier 0.58 48.0 3.10e-01 100.0% 25.2%
3909150 5063.1.1.15 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › OCIA 0.57 47.0 4.37e-01 100.0% 85.3%
4961052 2498.1.1.160 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_MA_2 0.54 41.0 2.74e-01 83.9% 19.2%
3740847 3812.1.1.14 ↗ alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › DUF1977 0.54 39.0 3.81e-01 78.6% 72.3%
3387885 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 38.0 3.64e-01 78.6% 66.2%
3931010 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.51 44.0 2.88e-01 100.0% 80.7%
D6 medium residues 451-489_608-682
PDB
Domain cluster: representative
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF25649.1 best Rotavirus_VP2 119.9 1.20e-34 70.2% 7.7%
PF25649.1 Rotavirus_VP2 40.3 1.40e-10 34.2% 3.9%
D7 medium residues 490-607
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25649.1 best Rotavirus_VP2 145.9 1.70e-42 100.0% 11.4%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2pbeA02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.53 34.0 3.34e-01 98.3% 58.7%
4ceiA03 6.10.250.2380 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.52 35.0 3.57e-01 99.2% 69.6%
1f7uA02 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.52 35.0 3.48e-01 85.6% 63.2%
4ivnA01 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 0.52 27.0 3.19e-01 86.4% 73.7%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4990103 601.7.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.59 41.0 4.08e-01 91.5% 70.0%
3466238 206.1.1.14 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › ABC1 0.57 43.0 2.92e-01 80.5% 22.4%
4436275 632.1.1.32 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › TMEM208_SND2 0.55 42.0 4.27e-01 91.5% 83.5%
4470601 601.7.1.35 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › UFL1_C 0.54 43.0 4.20e-01 86.4% 77.7%
5039337 601.7.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.53 44.0 4.22e-01 89.0% 78.5%
D8 medium residues 683-798
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25649.1 best Rotavirus_VP2 130.8 6.10e-38 100.0% 11.8%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4k0dA00 1.20.120.1730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.57 40.0 3.80e-01 73.3% 86.7%
6grjB01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.56 42.0 3.16e-01 78.4% 90.4%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5062917 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 35.0 3.39e-01 71.6% 80.8%
D9 medium residues 799-936
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25649.1 best Rotavirus_VP2 171.6 2.90e-50 100.0% 13.9%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2589759 4064.1.1.2 ↗ a+b complex topology › Inner layer core protein p3-related › Inner layer core protein p3-related › Inner layer core protein p3-related › Rota_VP2 0.73 64.0 3.85e-01 100.0% 15.5%