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RNA-dependent_RNA_polymerase

Euk-Vir

Changjiang_narna-like_virus_2

RNA-dependent_RNA_polymerase__YP_009337311__Changjiang_narna-like_virus_2__1922777

Identity

Accession:
YP_009337311 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

69.9 mean pLDDT

Cluster

View cluster (39 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 1-62_103-113
PDB
D2 medium residues 114-243
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3vkgA09 1.20.920.30 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.64 46.0 4.52e-01 100.0% 68.1%
2k3oA00 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.59 41.0 4.18e-01 100.0% 72.9%
5ko4A00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.57 42.0 4.70e-01 98.5% 100.0%
1jvmB00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 31.0 3.49e-01 97.7% 67.0%
6vw7B03 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.56 35.0 4.18e-01 98.5% 96.4%
1fc6A01 3.30.750.44 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.56 39.0 4.37e-01 96.9% 94.9%
2yw5A00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.55 44.0 4.31e-01 100.0% 79.0%
1wh4A01 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.55 32.0 3.69e-01 94.6% 77.7%
1n1fA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.55 41.0 3.89e-01 100.0% 66.0%
3f4mA00 1.20.1440.160 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tumor necrosis factor alpha-induced protein 8-like 0.55 46.0 4.45e-01 96.2% 100.0%
3ipiA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.54 40.0 3.18e-01 78.5% 43.7%
1kn1B00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.54 39.0 3.66e-01 100.0% 60.9%
5n17A01 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.53 39.0 4.29e-01 100.0% 95.2%
1vnsA01 1.20.144.10 Mainly Alpha › Up-down Bundle › Vanadium-containing Chloroperoxidase; domain 1 › Phosphatidic acid phosphatase type 2/haloperoxidase 0.52 47.0 4.26e-01 98.5% 74.9%
5c8gB00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.52 40.0 4.26e-01 99.2% 90.6%
7p5hB03 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.52 33.0 3.82e-01 98.5% 91.0%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.51 34.0 3.70e-01 88.5% 80.6%
1grlB01 1.10.560.10 Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain 0.51 44.0 3.72e-01 100.0% 95.9%
3o7qA02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.51 45.0 3.99e-01 97.7% 88.5%
7z7vF03 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.50 31.0 3.61e-01 87.7% 90.9%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3858496 387.1.6.2 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Conotoxin Mo3964 › Sin3a_C 0.64 46.0 4.13e-01 73.8% 87.8%
3413725 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.61 31.0 2.57e-01 100.0% 29.1%
3963081 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.59 40.0 3.88e-01 76.9% 60.7%
4015582 149.1.1.0 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 0.58 47.0 3.38e-01 86.9% 58.9%
3471942 5051.1.1.0 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like 0.54 43.0 3.01e-01 86.2% 53.0%
3640046 4120.1.1.0 ↗ few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP 0.54 40.0 3.61e-01 76.2% 100.0%
4169514 5050.1.1.54 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Mntp 0.54 48.0 4.33e-01 100.0% 97.8%
3446958 109.4.1.349 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RIX1 0.53 47.0 3.55e-01 99.2% 39.7%
2512676 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.53 40.0 3.32e-01 92.3% 43.3%
3165238 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.53 46.0 4.07e-01 95.4% 88.9%
4665328 1079.1.1.13 ↗ alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Mntp 0.51 41.0 3.90e-01 87.7% 80.0%
3336273 1134.1.2.19 ↗ alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Archaeal C-Ala helical domain › GIL1_IRKI_C 0.51 44.0 3.56e-01 100.0% 62.1%
3291710 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.51 45.0 3.52e-01 98.5% 85.2%
3660838 3121.1.1.12 ↗ a+b duplicates or obligate multimers › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › GIL1_IRKI_C 0.51 45.0 3.34e-01 100.0% 43.5%
4927849 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.50 35.0 3.39e-01 70.0% 95.9%
3273971 5050.1.1.1 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.50 45.0 3.87e-01 100.0% 76.7%
3695521 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.50 45.0 3.11e-01 100.0% 75.0%
4224874 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.50 33.0 3.53e-01 88.5% 75.7%
D3 medium residues 244-263_287-325_360-460_526-563
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337775__Hubei_narna-like_virus_21__1922952__D110-165_177-251_312-348
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2p92A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.51 23.0 3.09e-01 89.9% 81.1%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3598902 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.52 44.0 3.56e-01 89.9% 54.7%
3615272 304.48.1.25 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 0.52 44.0 3.54e-01 89.9% 54.0%
3792091 304.48.1.25 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RRM_4 0.52 44.0 3.66e-01 89.9% 52.5%
D4 medium residues 264-286_461-525_564-667
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337087__Hubei_narna-like_virus_4__1922958__D375-415_481-588
D5 medium residues 684-777
PDB
Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_009337159__Wenling_narna-like_virus_3__1923503__D602-722
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1tjcA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.57 42.0 4.19e-01 94.7% 77.9%
2o5hA00 1.10.3510.10 Mainly Alpha › Orthogonal Bundle › NMB0513-like › NMB0513-like 0.54 39.0 3.62e-01 77.7% 78.9%
3eslA02 1.25.40.930 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.54 41.0 3.87e-01 83.0% 89.1%
4i4cB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 45.0 3.06e-01 100.0% 52.5%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3886167 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 46.0 3.73e-01 92.6% 93.8%
D6 medium residues 778-811_825-857_870-916
PDB