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RNA-directed_RNA_polymerase_nsP4

Euk-Vir

Venezuelan_equine_encephalitis_virus

RNA-directed_RNA_polymerase_nsP4__NP_740699__Venezuelan_equine_encephalitis_virus__11036

Identity

Accession:
NP_740699 ↗
Protein ID:
RNA-directed_RNA_polymerase_nsP4
Kingdom:
euk

Quality

77.5 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Martellivirales› Togaviridae› Alphavirus› Venezuelan_equine_encephalitis_virus

TaxID: 11036

Cluster

View cluster (32 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 26-100
PDB
D2 medium residues 105-138_177-209_504-606
PDB
Domain cluster: rep: hypothetical_protein__YP_009337242__Hubei_virga-like_virus_11__1923326__D570-604_623-662_810-820_945-1065
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 59.2 5.00e-16 55.9% 21.6%
PF00978.27 RdRP_2 34.7 1.40e-08 31.8% 9.3%
D3 medium residues 210-245_321-340_376-409_424-451
PDB
Domain cluster: rep: ORF_1b__YP_003289291__Strawberry_pallidosis-associated_virus__227507__D117-174_213-235_276-309
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 35.6 7.30e-09 53.4% 17.1%
D4 medium residues 246-320_410-423
PDB
Domain cluster: rep: nsp4_nonstructural_protein_-putative_start-_putative__NP_740669__Sindbis_virus__11034__D271-320_413-429
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 53.1 3.40e-14 98.9% 16.8%
D5 medium residues 341-375_452-503
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009345057__Xinzhou_nematode_virus_7__1923775__D238-258_337-401
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 41.9 8.80e-11 59.8% 10.0%
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3gqcC01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.74 53.0 4.50e-01 74.7% 71.5%
5wm1A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.71 52.0 4.85e-01 78.2% 87.2%
6zxbA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.70 61.0 5.20e-01 96.6% 94.4%
2x3gA00 3.30.70.1910 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 56.0 5.13e-01 88.5% 87.9%
3tvkA00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.69 61.0 4.92e-01 100.0% 76.2%
4kgmA00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.67 49.0 3.58e-01 75.9% 54.8%
3w3sA01 3.30.70.1920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 47.0 3.80e-01 73.6% 83.3%
1bgxT05 3.30.70.370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 53.0 4.77e-01 100.0% 100.0%
3dcaA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 42.0 3.71e-01 73.6% 84.6%
1mwyA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 42.0 4.48e-01 74.7% 100.0%
5cqgA04 3.30.70.2630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 51.0 4.80e-01 98.9% 82.1%
3dh3A02 3.30.2350.10 Alpha Beta › 2-Layer Sandwich › Pseudouridine synthase › Pseudouridine synthase 0.58 40.0 3.23e-01 72.4% 45.3%
3r8yA01 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.57 37.0 4.12e-01 70.1% 86.4%
1lfpA03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.57 38.0 4.06e-01 70.1% 97.3%
1r89A03 3.30.70.590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Poly(A) polymerase predicted RNA binding domain 0.56 44.0 3.96e-01 89.7% 89.6%
1jqgA01 3.30.70.340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like 0.56 39.0 3.94e-01 74.7% 85.7%
1o5wB02 3.90.660.10 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › 0.56 48.0 3.92e-01 98.9% 79.3%
1a66A00 2.60.40.340 Mainly Beta › Sandwich › Immunoglobulin-like › Rel homology domain (RHD), DNA-binding domain 0.54 38.0 3.07e-01 73.6% 61.2%
3bv8A00 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.54 38.0 3.88e-01 73.6% 78.8%
2fpnA01 3.30.2030.10 Alpha Beta › 2-Layer Sandwich › TBP-like › YwmB-like 0.54 37.0 3.26e-01 71.3% 84.3%
3d68A01 3.30.70.340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like 0.54 38.0 3.82e-01 75.9% 87.0%
1zvpD00 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.54 37.0 3.26e-01 71.3% 76.3%
1vioA03 3.30.70.1560 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Alpha-L RNA-binding motif 0.54 37.0 3.85e-01 72.4% 100.0%
4ab7H02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 36.0 3.01e-01 96.6% 40.1%
2xhcA01 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.53 37.0 3.63e-01 73.6% 89.5%
1g1kA00 2.60.40.680 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 37.0 3.19e-01 72.4% 86.7%
2ww4A02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.52 37.0 3.39e-01 75.9% 95.8%
6fijA02 3.40.366.10 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 0.52 40.0 2.82e-01 86.2% 33.6%
5edxA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 36.0 3.33e-01 72.4% 86.8%
2y23A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 36.0 3.46e-01 73.6% 82.7%
2f06A00 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.51 40.0 3.44e-01 86.2% 77.1%
2nyhA00 3.30.70.1240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › DOPA-like domains 0.51 36.0 3.34e-01 74.7% 92.2%
2jfdA03 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.51 35.0 3.87e-01 73.6% 100.0%
3n28A02 3.30.70.2020 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 43.0 4.12e-01 97.7% 88.7%
2kdoA03 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 36.0 3.76e-01 74.7% 92.5%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3274989 304.1.1.0 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain 0.63 43.0 3.58e-01 71.3% 91.3%
2066826 304.107.1.0 ↗ a+b two layers › Alpha-beta plaits › Aminomethyltransferase folate-binding domain › Aminomethyltransferase folate-binding domain 0.63 43.0 4.22e-01 70.1% 96.8%
4957085 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.62 42.0 4.78e-01 70.1% 98.5%
4945098 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.61 43.0 4.50e-01 73.6% 96.2%
4632150 304.56.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like 0.61 44.0 4.35e-01 77.0% 87.4%
5047332 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.61 43.0 4.50e-01 73.6% 86.3%
138899 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.61 43.0 4.53e-01 74.7% 95.0%
4935066 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.61 41.0 4.06e-01 70.1% 92.6%
5057396 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.61 42.0 4.48e-01 72.4% 97.3%
5009733 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 0.60 54.0 4.36e-01 98.9% 87.9%
5004481 304.11.1.16 ↗ a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase › DUF2110_C 0.60 41.0 4.26e-01 70.1% 92.4%
5046295 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.59 43.0 4.18e-01 77.0% 86.0%
5065444 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.59 43.0 4.10e-01 78.2% 86.7%
3428826 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.59 42.0 4.33e-01 74.7% 95.0%
3333353 304.3.1.1 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.58 42.0 4.50e-01 77.0% 100.0%
4053590 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.58 41.0 3.66e-01 74.7% 86.8%
4064506 304.147.1.1 ↗ a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.58 37.0 4.27e-01 70.1% 93.3%
3313982 304.3.1.1 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.58 43.0 4.39e-01 80.5% 90.6%
4072241 304.107.1.1 ↗ a+b two layers › Alpha-beta plaits › Aminomethyltransferase folate-binding domain › Aminomethyltransferase folate-binding domain › GCV_T 0.57 43.0 2.97e-01 81.6% 33.2%
5066414 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.57 39.0 4.04e-01 70.1% 91.3%
4949564 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.57 38.0 4.46e-01 70.1% 100.0%
4132664 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.57 43.0 3.77e-01 79.3% 90.4%
4934123 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.57 38.0 4.40e-01 70.1% 100.0%
2507085 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.56 38.0 4.28e-01 72.4% 95.2%
5227 304.7.1.1 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Propep_M14 0.56 39.0 3.93e-01 74.7% 84.8%
4215974 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 0.55 40.0 4.36e-01 75.9% 95.7%
3958083 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.55 46.0 3.10e-01 94.3% 91.5%
197838 304.147.1.1 ↗ a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.55 38.0 3.90e-01 73.6% 78.8%
4439117 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.53 39.0 3.52e-01 79.3% 89.1%
3970056 304.1.1.0 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain 0.52 37.0 3.42e-01 74.7% 98.3%
4021179 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 37.0 2.31e-01 75.9% 51.5%
3281169 304.11.1.12 ↗ a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase › WCX 0.52 35.0 3.76e-01 70.1% 80.0%
4933530 304.24.1.5 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N 0.52 36.0 3.82e-01 73.6% 90.7%
4950919 11.1.1.257 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Top6b_C 0.51 36.0 3.38e-01 72.4% 61.9%
4319410 304.15.1.7 ↗ a+b two layers › Alpha-beta plaits › Viral DNA-binding domain › Viral DNA-binding domain › DUF5609 0.51 42.0 4.32e-01 94.3% 98.8%
4265513 304.147.1.1 ↗ a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.50 33.0 3.66e-01 70.1% 96.7%
3164278 304.8.1.25 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DUF5609 0.50 40.0 4.04e-01 89.7% 93.3%