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RNA-dependent_RNA_polymerase

Euk-Vir

Infectious_bronchitis_virus

RNA-dependent_RNA_polymerase__NP_740629__Infectious_bronchitis_virus__11120

Identity

Accession:
NP_740629 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

87.5 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Pisoniviricetes› Nidovirales› Coronaviridae› Gammacoronavirus› Infectious_bronchitis_virus

TaxID: 11120

Cluster

View cluster (23 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 1-127
PDB
Domain cluster: rep: nsp12__YP_008439222__Bat_coronavirus_CDPHE15_USA_2006__1384461__D18-119
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF06478.20 best CoV_RPol_N 121.9 4.50e-35 85.8% 30.3%
D2 medium residues 128-266
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF06478.20 best CoV_RPol_N 212.5 1.30e-62 100.0% 38.3%
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zarA03 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.68 42.0 4.90e-01 95.7% 87.6%
2qkwB02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.56 52.0 4.58e-01 99.3% 99.0%
3bjdA01 1.10.1240.20 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Lytic transglycosylase, superhelical linker domain 0.54 29.0 3.47e-01 96.4% 78.4%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2994348 304.48.1.9 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1,CoV_RPol_N 0.97 92.0 5.36e-01 100.0% 14.5%
3482553 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.61 55.0 3.95e-01 97.8% 45.9%
5059224 206.1.1.17 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Kdo 0.55 44.0 3.88e-01 95.7% 57.6%
4135745 7577.1.1.4 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Pyridoxal_deC 0.51 37.0 2.59e-01 76.3% 81.8%
D3 medium residues 267-332
PDB
Domain cluster: rep: coronavirus_nsp9_-RdRp-__NP_742138__Bovine_coronavirus__11128__D257-321
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF06478.20 best CoV_RPol_N 121.2 7.30e-35 100.0% 18.6%
D4 medium residues 333-394
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF06478.20 best CoV_RPol_N 60.4 2.20e-16 69.3% 12.3%
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4akgA03 3.20.180.20 Alpha Beta › Alpha-Beta Barrel › Split barrel-like › Dynein motor heavy chain, linker domain, subdomain 3 0.57 36.0 3.27e-01 85.5% 47.0%
3v9oA00 3.30.1130.10 Alpha Beta › 2-Layer Sandwich › GTP Cyclohydrolase I, domain 2 › GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain 0.55 45.0 3.80e-01 100.0% 95.0%
1dpbA00 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.53 45.0 3.09e-01 100.0% 37.4%
3dmgA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 44.0 3.23e-01 98.4% 50.0%
1auuA00 2.30.24.10 Mainly Beta › Roll › Transcription Regulation, Sacy; Chain A › CAT RNA-binding domain 0.52 33.0 3.48e-01 91.9% 72.7%
4pj2A00 2.40.128.460 Mainly Beta › Beta Barrel › Lipocalin › Periplasmic lysozyme inhibitor of I-type lysozyme 0.51 38.0 3.15e-01 82.3% 95.0%
3cpxA02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.51 28.0 2.85e-01 96.8% 51.6%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2994348 304.48.1.9 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1,CoV_RPol_N 0.93 87.0 4.72e-01 100.0% 6.7%
3715372 6110.1.1.1 ↗ alpha superhelices › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain › DHC_N2 0.54 43.0 2.76e-01 87.1% 18.4%
3209662 223.1.1.23 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.53 40.0 2.78e-01 100.0% 22.0%
D5 medium residues 414-451_840-940
PDB
Domain cluster: rep: NSP12__YP_009825029__Duck_coronavirus__300188__D836-945
D6 medium residues 452-466_500-540_557-587
PDB
Domain cluster: rep: putative_coronavirus_nsp9_-RdRp-__NP_839965__Porcine_epidemic_diarrhea_virus__28295__D437-453_491-565
D7 medium residues 588-652_702-839
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1s48A04 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.80 45.0 6.02e-01 90.6% 100.0%
1gx5A03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.78 47.0 6.07e-01 90.1% 100.0%
1khvA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.75 48.0 6.01e-01 88.7% 100.0%
1s7hA01 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.72 30.0 4.75e-01 79.3% 100.0%
1lfpA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.69 26.0 4.31e-01 77.3% 95.9%
2iboA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 31.0 4.56e-01 83.3% 100.0%
1mw7A03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.66 27.0 4.25e-01 85.7% 100.0%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.63 28.0 3.14e-01 72.9% 49.1%
1vk8A00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 29.0 4.14e-01 84.2% 98.9%
2bk8A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 25.0 3.42e-01 70.4% 76.3%
1yqhA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 30.0 4.04e-01 85.2% 93.3%
4erdA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 28.0 3.71e-01 83.3% 82.4%
1lxjA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 30.0 4.03e-01 84.2% 94.2%
2kviA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 25.0 3.81e-01 70.9% 100.0%
1s12A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.58 27.0 3.71e-01 70.0% 90.4%
2wp3O00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 24.0 3.35e-01 71.4% 78.4%
6h4lA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 24.0 3.35e-01 71.4% 79.2%
1zvpD00 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.56 28.0 3.46e-01 72.9% 74.0%
2xy1A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 25.0 3.46e-01 71.4% 85.6%
4q5eA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.55 20.0 3.21e-01 87.2% 86.7%
1zhvA00 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.54 30.0 3.59e-01 79.3% 80.6%
2fm8B00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.51 25.0 3.08e-01 70.4% 71.2%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2994348 304.48.1.9 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1,CoV_RPol_N 0.98 96.0 5.90e-01 100.0% 27.1%
4875416 304.48.1.13 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flavi_NS5 0.69 66.0 5.17e-01 100.0% 57.7%
3350779 304.126.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in vacuolar ATP synthase subunit C › ferredoxin-like domain in vacuolar ATP synthase subunit C 0.67 28.0 4.32e-01 84.2% 96.2%
3781133 304.24.1.7 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › V_ATPase_I 0.66 27.0 4.16e-01 83.3% 93.8%
4379259 304.48.1.6 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_A 0.64 35.0 4.69e-01 78.3% 99.1%
3895104 304.24.1.7 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › V_ATPase_I 0.63 27.0 3.49e-01 80.3% 67.0%
3974380 304.154.1.0 ↗ a+b two layers › Alpha-beta plaits › Regulator of polyketide synthase expression N-terminal domain › Regulator of polyketide synthase expression N-terminal domain 0.62 35.0 4.18e-01 91.1% 81.5%
3953208 305.2.1.1 ↗ a+b two layers › DCoH-like › Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) › Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) › Pterin_4a 0.61 24.0 3.49e-01 70.0% 76.6%
4882532 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 0.59 53.0 4.42e-01 93.1% 59.8%
3639504 305.2.1.1 ↗ a+b two layers › DCoH-like › Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) › Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) › Pterin_4a 0.59 27.0 3.56e-01 78.8% 77.3%
3766383 304.48.1.6 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_A 0.59 34.0 4.35e-01 80.3% 96.7%
3611027 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.58 25.0 3.84e-01 70.0% 100.0%
3971738 304.8.1.102 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_3, ACT_7 0.58 29.0 3.63e-01 72.4% 76.6%
5036198 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.57 22.0 3.47e-01 71.9% 95.7%
4956603 327.11.2.13 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_PNO1_2nd 0.56 28.0 3.46e-01 77.8% 74.4%
3608339 304.48.1.6 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_A 0.54 34.0 4.02e-01 76.8% 93.3%
3922338 101.1.2.512 ↗ alpha arrays › HTH › HTH › winged helix domain › PF25877 0.52 21.0 3.17e-01 72.4% 88.7%
4241274 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 48.0 3.76e-01 100.0% 69.9%
5041218 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 0.50 26.0 3.22e-01 71.4% 76.9%
4643231 304.48.1.39 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › MatK_N 0.50 41.0 3.61e-01 85.7% 70.7%
4665681 304.48.1.39 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › MatK_N 0.50 42.0 3.70e-01 88.2% 98.0%