←Back to structures

RNA-dependent_RNA_polymerase

Euk-Vir

Chickpea_chlorotic_stunt_virus

RNA-dependent_RNA_polymerase__YP_667838__Chickpea_chlorotic_stunt_virus__328430

Identity

Accession:
YP_667838 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

75.8 mean pLDDT

Cluster

View cluster (38 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 93-191
PDB
Domain cluster: rep: P1_protein__YP_667839__Chickpea_chlorotic_stunt_virus__328430__D113-193
D2 high residues 225-395
PDB
Domain cluster: rep: 100_kDa_protein__YP_008130303__Citrus_vein_enation_virus__1301220__D379-571
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02122.22 best Peptidase_S39 223.7 2.40e-66 100.0% 84.2%
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zyoA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.79 41.0 5.39e-01 100.0% 87.1%
3otpA01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.78 73.0 6.85e-01 99.4% 88.7%
4ri0A01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.76 72.0 6.82e-01 100.0% 86.9%
1hpgA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.69 39.0 5.09e-01 100.0% 96.0%
1boqA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.65 39.0 4.92e-01 99.4% 96.3%
2sfaA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.61 34.0 4.48e-01 84.8% 100.0%
2diqA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.59 25.0 3.25e-01 100.0% 67.0%
1fx0B01 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.59 28.0 3.98e-01 73.1% 96.2%
3mp6A05 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.58 20.0 3.24e-01 84.2% 82.5%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2472950 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.86 83.0 8.02e-01 100.0% 94.6%
2710030 1.1.5.12 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_S39 0.85 81.0 7.79e-01 100.0% 90.6%
260 1.1.5.22 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_S32 0.84 67.0 6.36e-01 98.2% 71.2%
1290831 1.1.17.9 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › PF30586 0.82 78.0 6.58e-01 100.0% 84.2%
4028467 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.80 75.0 6.27e-01 98.2% 68.0%
3452728 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.80 76.0 7.07e-01 100.0% 93.2%
3650249 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.80 76.0 6.58e-01 100.0% 81.2%
4205419 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.79 75.0 6.71e-01 100.0% 89.6%
3816593 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.79 74.0 6.69e-01 98.2% 87.7%
4647114 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.79 74.0 6.53e-01 99.4% 80.8%
4625374 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.78 74.0 6.61e-01 99.4% 84.3%
3464880 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.78 74.0 6.75e-01 99.4% 85.1%
3213725 1.1.17.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › DUF316 0.78 73.0 6.14e-01 100.0% 85.0%
3448106 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.77 73.0 6.35e-01 100.0% 86.0%
257 1.1.5.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_C4 0.77 71.0 6.51e-01 98.2% 78.1%
3280223 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.75 69.0 6.59e-01 97.1% 89.7%
22055 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.74 68.0 6.52e-01 95.9% 93.2%
3277840 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.74 67.0 6.31e-01 95.9% 88.2%
4119987 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.74 68.0 6.15e-01 98.2% 87.1%
4015954 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.73 68.0 6.02e-01 99.4% 87.7%
4614564 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.71 64.0 6.15e-01 95.9% 86.7%
4655762 1.1.17.21 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Peptidase_S55 0.70 60.0 5.65e-01 91.2% 93.7%
4319764 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.59 28.0 3.45e-01 73.1% 69.1%
3936885 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 22.0 3.43e-01 70.8% 98.5%
3508441 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.51 25.0 3.23e-01 88.3% 81.1%
D3 high residues 1037-1089
PDB
Domain cluster: rep: putative_protein_P2__YP_001931931__Tobacco_vein_distorting_virus__192203__D1031-1055_1057-1076_1079-1084
D4 medium residues 590-858_938-959
PDB
Domain cluster: rep: NIb__YP_009221991__Jasmine_virus_T__1775963__D1-51_64-80_112-210_276-312
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 159.0 2.80e-46 75.6% 50.3%
D5 medium residues 893-937_960-1021
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 66.5 3.30e-18 72.0% 17.6%
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7uinD01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.67 60.0 5.17e-01 100.0% 71.9%
1gmuA01 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.65 38.0 4.57e-01 99.1% 91.0%
6qwtA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.64 55.0 4.97e-01 100.0% 68.1%
1earA02 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.64 37.0 4.46e-01 99.1% 88.4%
3cjsA00 3.30.70.1170 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sun protein; domain 3 0.62 34.0 4.25e-01 97.2% 94.8%
3kzxA02 1.10.150.730 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.61 36.0 4.51e-01 80.4% 100.0%
3mahA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.61 39.0 4.70e-01 95.3% 100.0%
2qyxB01 3.30.70.1360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › mj0159-like 0.61 39.0 3.94e-01 99.1% 64.2%
2yx1A01 3.30.70.2580 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 36.0 4.25e-01 99.1% 97.0%
1ufwA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.58 42.0 4.38e-01 96.3% 84.2%
1weyA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.58 42.0 4.29e-01 98.1% 77.9%
2lxiA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 43.0 4.64e-01 98.1% 92.3%
5cy0A00 3.30.30.10 Alpha Beta › 2-Layer Sandwich › Defensin A-like › Knottin, scorpion toxin-like 0.57 32.0 3.93e-01 95.3% 92.1%
2j0wA04 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.54 37.0 4.22e-01 95.3% 100.0%
4hkqA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.53 41.0 3.80e-01 100.0% 63.9%
1f7uA03 3.30.1360.70 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Arginyl tRNA synthetase N-terminal domain 0.52 42.0 3.92e-01 86.9% 80.6%
4lvnP00 3.30.70.2380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 36.0 3.96e-01 97.2% 96.3%
5wm1A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.51 40.0 4.02e-01 98.1% 82.6%
2hfqA00 3.10.510.10 Alpha Beta › Roll › NE1680-like fold › NE1680-like 0.51 33.0 3.72e-01 94.4% 84.7%
1u0sA00 3.30.70.1110 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Histidine kinase CheA-like, P2 response regulator-binding domain 0.51 37.0 4.09e-01 96.3% 97.7%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3483524 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 0.78 71.0 5.10e-01 100.0% 48.9%
3479114 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 0.78 71.0 4.33e-01 100.0% 23.0%
3495499 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 0.77 70.0 5.03e-01 100.0% 47.2%
3479534 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 0.77 70.0 4.64e-01 100.0% 41.9%
4289835 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 0.71 65.0 5.15e-01 100.0% 85.7%
3615476 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 0.70 63.0 4.43e-01 98.1% 45.2%
3068775 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 0.70 63.0 5.10e-01 100.0% 63.5%
3651060 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 63.0 5.17e-01 100.0% 93.2%
4472004 304.22.1.1 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C 0.65 38.0 4.35e-01 99.1% 81.3%
3947863 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 0.64 57.0 4.37e-01 100.0% 60.4%
4948795 304.5.1.2 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF190 0.61 41.0 4.69e-01 98.1% 97.3%
4174001 304.22.1.1 ↗ a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C 0.61 36.0 4.31e-01 99.1% 95.4%
4280715 387.1.5.3 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like › Toxin_3 0.60 31.0 4.09e-01 86.9% 96.4%
4965997 4955.1.1.0 ↗ a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.59 39.0 4.21e-01 88.8% 80.0%
3716388 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.59 39.0 3.80e-01 98.1% 61.7%
3927796 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 0.58 53.0 3.92e-01 100.0% 43.4%
3270164 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 26.0 3.29e-01 99.1% 69.2%
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 0.57 52.0 3.91e-01 100.0% 43.8%
3710757 304.163.1.1 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain › R1_ABCA1 0.57 37.0 4.32e-01 93.5% 100.0%
3880483 310.1.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain 0.56 32.0 3.15e-01 81.3% 49.6%
4051474 387.1.5.3 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like › Toxin_3 0.55 37.0 4.33e-01 98.1% 100.0%
3816901 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.54 28.0 3.64e-01 86.0% 96.4%
5083546 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.54 38.0 4.26e-01 99.1% 100.0%
4971836 304.48.1.22 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GCH_III 0.52 40.0 4.06e-01 98.1% 81.8%
4590617 3435.1.1.2 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC › CENP-N 0.50 36.0 3.78e-01 74.8% 86.3%