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P2

Euk-Vir

Maize_yellow_dwarf_virus-RMV2

P2__YP_009249569__Maize_yellow_dwarf_virus-RMV2__1833824

Identity

Accession:
YP_009249569 ↗
Protein ID:
P2
Kingdom:
euk

Quality

91.9 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Pisoniviricetes› Sobelivirales› Solemoviridae› Polerovirus› Maize_yellow_dwarf_virus-RMV2

TaxID: 1833824

Cluster

View cluster (85 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 261-318
PDB
Domain cluster: rep: putative_protein_P2__YP_001931931__Tobacco_vein_distorting_virus__192203__D1031-1055_1057-1076_1079-1084
D2 medium residues 1-78_127-189
PDB
Domain cluster: rep: hypothetical_protein_3__YP_009345007__Wuhan_spider_virus_8__1923757__D1-105_147-200
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 66.7 2.90e-18 55.3% 17.2%
PF02123.22 RdRP_4 45.7 6.40e-12 46.1% 17.2%
D3 medium residues 79-126_247-260
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7jtjA01 3.30.559.30 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Nonribosomal peptide synthetase, condensation domain 0.61 42.0 2.74e-01 71.0% 78.1%
1y7oB00 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.60 42.0 3.04e-01 72.6% 56.2%
2djpA00 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.57 33.0 3.07e-01 91.9% 44.2%
1a6jB00 3.40.930.10 Alpha Beta › 3-Layer(aba) Sandwich › Mannitol-specific EII; Chain A › Mannitol-specific EII; Chain A 0.56 42.0 3.21e-01 82.3% 72.0%
1j09A05 1.10.10.350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.55 44.0 3.81e-01 91.9% 54.1%
1fc3B00 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 0.54 40.0 3.45e-01 80.6% 64.4%
1miwA03 1.20.58.560 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 38.0 3.33e-01 100.0% 51.0%
3h0dB02 1.10.1200.150 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Transcriptional repressor of class III stress genes, C-terminal domain 0.51 40.0 3.74e-01 87.1% 92.6%
3fhdA01 1.20.120.860 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Herpesvirus alkaline exonuclease, N-terminal domain 0.51 41.0 3.41e-01 100.0% 99.3%
2r5uC00 1.10.860.10 Mainly Alpha › Orthogonal Bundle › DNAb Helicase; Chain A › DNAb Helicase; Chain A 0.51 39.0 3.16e-01 88.7% 61.6%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4331679 103.13.1.0 ↗ alpha arrays › RuvA-C › C-terminal lid domain of glucokinase regulatory protein › C-terminal lid domain of glucokinase regulatory protein 0.67 47.0 4.41e-01 74.2% 81.3%
3994858 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.64 43.0 4.03e-01 71.0% 65.0%
3396459 2488.1.1.19 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › PF27710 0.62 42.0 2.95e-01 71.0% 34.3%
3615365 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.53 36.0 2.56e-01 74.2% 24.3%
D4 medium residues 190-246
PDB
Domain cluster: rep: uncovered_polypeptide_polyprotein_P2ab__YP_002158813_394-928__Sowbane_mosaic_virus__378833__D364-413
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 68.7 6.90e-19 100.0% 14.6%
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1konA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.73 54.0 4.98e-01 80.7% 69.3%
2a2cA02 3.30.70.3170 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 60.0 5.29e-01 96.5% 83.3%
3fryA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 57.0 5.52e-01 96.5% 90.6%
3pyfA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.68 58.0 4.43e-01 98.2% 86.1%
4uskA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.67 56.0 4.26e-01 100.0% 81.2%
3v2uC02 3.30.70.3170 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 56.0 4.83e-01 98.2% 85.3%
4dezA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.66 52.0 4.50e-01 93.0% 75.8%
3tufA00 1.10.287.4300 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Stage III sporulation protein AH-like 0.66 55.0 4.36e-01 93.0% 60.9%
1ufwA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.64 54.0 4.72e-01 100.0% 73.7%
7xx8A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.63 51.0 4.64e-01 94.7% 84.0%
3g98A00 3.10.310.40 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › 0.62 48.0 3.93e-01 87.7% 60.4%
3dbaA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.61 46.0 3.37e-01 84.2% 84.8%
1wf1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 48.0 4.32e-01 98.2% 71.1%
1l0wA03 3.30.1360.30 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › GAD-like domain 0.58 46.0 3.54e-01 89.5% 58.7%
5cy0A00 3.30.30.10 Alpha Beta › 2-Layer Sandwich › Defensin A-like › Knottin, scorpion toxin-like 0.58 40.0 3.97e-01 89.5% 68.3%
4rpfA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.58 46.0 3.67e-01 94.7% 89.5%
1s79A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 47.0 4.01e-01 100.0% 68.9%
1omyA00 3.30.30.10 Alpha Beta › 2-Layer Sandwich › Defensin A-like › Knottin, scorpion toxin-like 0.57 41.0 4.01e-01 86.0% 70.3%
1s7hA02 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 47.0 4.28e-01 100.0% 80.5%
2i61A00 3.30.30.10 Alpha Beta › 2-Layer Sandwich › Defensin A-like › Knottin, scorpion toxin-like 0.56 39.0 3.85e-01 82.5% 67.7%
3nuiA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.55 44.0 3.47e-01 96.5% 50.7%
1f7uA03 3.30.1360.70 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Arginyl tRNA synthetase N-terminal domain 0.55 41.0 3.24e-01 84.2% 60.4%
1yg2A01 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 0.55 40.0 3.57e-01 87.7% 54.4%
3h7hB00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.54 44.0 3.90e-01 100.0% 75.8%
4hkjD00 2.60.240.30 Mainly Beta › Sandwich › Viral Chemokine Inhibitor; Chain A › 0.51 41.0 3.05e-01 100.0% 66.1%
2q07A02 3.10.450.90 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › ArcTGT, C2 domain 0.51 41.0 3.93e-01 89.5% 84.6%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5044483 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.72 40.0 3.27e-01 89.5% 31.0%
4112996 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.69 61.0 4.65e-01 100.0% 84.4%
4096485 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.69 58.0 3.86e-01 100.0% 27.3%
4241788 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.66 56.0 4.20e-01 98.2% 86.0%
5073695 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.65 56.0 4.59e-01 93.0% 87.0%
4051474 387.1.5.3 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like › Toxin_3 0.65 49.0 4.52e-01 98.2% 62.7%
4956226 304.120.1.6 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › ThiI_fer 0.65 54.0 5.04e-01 100.0% 90.7%
4100012 327.13.1.5 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif I in type III secretion system › Ring-building motif I in type III secretion system › SpoIIIAH 0.64 53.0 4.24e-01 93.0% 59.3%
4182084 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.63 50.0 4.33e-01 87.7% 92.2%
4994607 512.1.1.2 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_2nd 0.63 54.0 4.24e-01 93.0% 82.6%
4065305 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.63 52.0 4.18e-01 100.0% 89.6%
4280715 387.1.5.3 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like › Toxin_3 0.62 43.0 4.42e-01 89.5% 78.2%
4666603 5104.1.1.1 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.61 47.0 3.51e-01 87.7% 41.7%
3857454 246.3.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like 0.61 51.0 3.01e-01 98.2% 13.9%
5081436 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.60 48.0 4.20e-01 93.0% 60.0%
4298327 5104.1.1.1 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.60 46.0 3.68e-01 86.0% 54.0%
4970115 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.60 50.0 4.81e-01 100.0% 87.1%
3455460 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.60 46.0 2.86e-01 84.2% 38.8%
3749773 304.9.1.17 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › DUF1866 0.59 47.0 4.08e-01 98.2% 64.8%
5042647 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.58 38.0 3.10e-01 89.5% 34.5%
4029328 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.58 47.0 4.12e-01 100.0% 64.0%
5023739 1036.1.1.1 ↗ a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.58 46.0 3.92e-01 94.7% 81.0%
4932614 304.24.1.6 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › SBDS_C 0.56 43.0 4.09e-01 87.7% 82.9%
3255033 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.56 44.0 4.06e-01 98.2% 76.5%
4663148 109.4.1.1137 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CNOT10_TPR 0.55 43.0 2.37e-01 82.5% 52.7%
5027911 1036.1.1.1 ↗ a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.54 44.0 3.84e-01 100.0% 86.0%
4552919 306.2.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › arginine repressor C terminal domain-related › C-terminal domain of arginine repressor › Arg_repressor_C 0.53 41.0 3.66e-01 87.7% 78.8%
4503771 3009.1.1.1 ↗ alpha arrays › Insertion subdomain in DsbA-like › Insertion subdomain in DsbA-like › Insertion subdomain in DsbA-like › DSBA 0.53 39.0 2.85e-01 84.2% 51.1%
3717353 859.1.1.0 ↗ a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 0.52 40.0 2.83e-01 86.0% 76.8%