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RNA-dependent_RNA_polymerase

Euk-Vir

Golden_shiner_totivirus

RNA-dependent_RNA_polymerase__YP_009256209__Golden_shiner_totivirus__1856030

Identity

Accession:: YP_009256209 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

88.0 mean pLDDT

Cluster

View cluster (10 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 1-63

PDB

Domain cluster: representative

CATH (7)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5cwhA01	1.25.10.10	Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant	0.66	46.0	3.48e-01	74.6%	35.9%
5gl7A01	1.10.730.10	Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1	0.60	45.0	3.43e-01	84.1%	71.7%
4aifA00	1.25.40.10	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain	0.59	40.0	3.17e-01	71.4%	43.1%
2g1pA02	1.10.1020.10	Mainly Alpha › Orthogonal Bundle › Adenine-specific Methyltransferase; domain 2 › Adenine-specific Methyltransferase, Domain 2	0.57	43.0	3.82e-01	85.7%	55.0%
4etrB00	1.20.1260.10	Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle	0.54	45.0	3.79e-01	100.0%	60.7%
4zvaA00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.52	42.0	3.38e-01	100.0%	93.3%
4j0eA01	3.40.50.720	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain	0.51	43.0	3.12e-01	98.4%	93.6%

ECOD (12)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5048081	604.12.1.0 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain	0.69	48.0	4.58e-01	73.0%	77.3%
4978312	604.12.1.1 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT	0.67	46.0	4.48e-01	71.4%	78.6%
3340102	109.4.1.140 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › NatB_MDM20	0.66	51.0	3.56e-01	84.1%	29.0%
4972182	604.12.1.1 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT	0.65	45.0	4.40e-01	73.0%	82.9%
4977808	604.12.1.0 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain	0.65	45.0	4.37e-01	73.0%	88.6%
4446713	604.11.1.1 ↗	alpha bundles › Spectrin repeat-like › XseB-like › XseB-like › Exonuc_VII_S	0.64	48.0	4.59e-01	82.5%	73.3%
3423908	6155.1.1.0 ↗	alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter	0.62	48.0	4.19e-01	84.1%	84.2%
3692194	6155.1.1.0 ↗	alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter	0.61	48.0	4.45e-01	85.7%	80.0%
3578352	109.4.1.884 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ARM_UBP24_USP9X-Y	0.60	46.0	3.32e-01	84.1%	42.6%
3870961	109.4.1.498 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF4487	0.60	45.0	2.74e-01	84.1%	18.1%
3739924	6155.1.1.2 ↗	alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop	0.58	46.0	3.94e-01	87.3%	64.8%
3862034	6155.1.1.0 ↗	alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter	0.58	44.0	4.04e-01	84.1%	84.7%

D2 medium residues 64-94_181-309

PDB

Domain cluster: representative

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
6xz3A01	1.20.120.230	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like	0.61	26.0	3.02e-01	90.6%	51.3%
2nscA01	3.30.70.1050	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Trigger factor ribosome-binding domain	0.53	21.0	2.92e-01	78.1%	71.8%

ECOD (5)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4956683	604.1.1.0 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat	0.67	27.0	3.46e-01	88.1%	61.0%
3920672	206.1.1.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase	0.62	30.0	4.01e-01	77.5%	83.3%
3701882	331.4.1.0 ↗	a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1	0.57	32.0	3.90e-01	91.3%	88.4%
3684015	192.29.1.0 ↗	alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding)	0.57	30.0	3.75e-01	78.1%	82.0%
3921728	192.2.1.0 ↗	alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin	0.57	30.0	3.58e-01	77.5%	73.0%

D3 medium residues 457-520_559-588

PDB

Domain cluster: representative

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2glzA00	3.30.1330.130	Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; ›	0.56	42.0	3.74e-01	83.0%	96.0%
6ketA01	3.20.20.30	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain	0.51	40.0	2.78e-01	86.2%	89.3%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3802552	601.1.1.91 ↗	alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › DUF1218	0.51	36.0	3.06e-01	74.5%	97.6%
4928209	2004.1.1.233 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Cas3-like_C_2	0.51	40.0	2.51e-01	85.1%	58.8%