←Back to structures

RNA-dependent_RNA_polymerase,_partial

Euk-Vir

Persimmon_virus_B

RNA-dependent_RNA_polymerase,_partial__YP_009112883__Persimmon_virus_B__1493829

Identity

Accession:: YP_009112883 ↗
Protein ID:: RNA-dependent_RNA_polymerase,_partial
Kingdom:: euk

Quality

77.5 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Martellivirales› Closteroviridae› Olivavirus› Persimmon_virus_B

TaxID: 1493829

Cluster

View cluster (450 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 336-435

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase,_partial__YP_009241367__Grapevine_leafroll-associated_virus_13__1815581__D413-491

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00978.27 best	RdRP_2	38.2	1.10e-09	78.0%	17.5%

CATH (17)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2fu2A00	1.20.1440.50	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like	0.63	35.0	3.91e-01	75.0%	69.2%
4hhyC01	1.20.142.10	Mainly Alpha › Up-down Bundle › Poly(ADP-ribose) Polymerase; domain 1 › Poly(ADP-ribose) polymerase, regulatory domain	0.61	37.0	3.43e-01	100.0%	45.8%
1jalA03	1.10.150.300	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain	0.60	40.0	4.30e-01	86.0%	82.7%
2m3aA00	1.10.10.1900	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Knl-2 Myb-like DNA-binding domain-like	0.58	31.0	3.65e-01	94.0%	76.1%
4gf0A02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.56	40.0	3.84e-01	73.0%	70.8%
4udsA00	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.55	47.0	3.92e-01	99.0%	60.5%
3bcgA00	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.54	47.0	3.82e-01	100.0%	55.6%
3i2fA02	1.10.3020.10	Mainly Alpha › Orthogonal Bundle › alpha-amino acid ester hydrolase ( Helical cap domain) › alpha-amino acid ester hydrolase ( Helical cap domain)	0.54	36.0	3.69e-01	86.0%	70.5%
3rq9A00	1.10.287.2500	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.54	35.0	3.81e-01	95.0%	83.3%
3l9fA02	6.10.140.1570	Special › Helix non-globular › Helix Hairpins ›	0.53	37.0	4.06e-01	73.0%	98.8%
1rz4A01	1.25.40.250	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › ARM repeat; domain 1	0.53	30.0	2.86e-01	76.0%	43.3%
4fcyA01	1.10.10.60	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like	0.53	31.0	3.39e-01	94.0%	71.8%
3l8rA00	1.20.58.80	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit	0.52	40.0	3.99e-01	81.0%	85.3%
1vw4T01	6.10.330.20	Special › Helix non-globular › Monooxygenase ›	0.52	37.0	3.59e-01	83.0%	67.0%
2i2xB01	1.10.1240.10	Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain	0.51	34.0	3.48e-01	82.0%	68.0%
3rbtA02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.50	33.0	3.23e-01	73.0%	57.3%
1q8cA00	1.10.940.10	Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like	0.50	39.0	3.67e-01	99.0%	65.9%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3991087	133.1.1.1 ↗	alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF	0.61	44.0	3.58e-01	76.0%	61.0%
3775067	198.1.1.21 ↗	alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapA, SapB_2	0.59	41.0	3.89e-01	72.0%	73.3%
3716363	603.1.1.0 ↗	alpha bundles › STAT-like › t-snare proteins › t-snare proteins	0.58	51.0	4.06e-01	100.0%	86.7%
4009492	5059.1.1.1 ↗	alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA	0.55	44.0	3.23e-01	88.0%	67.8%
3701245	604.7.1.1 ↗	alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA	0.55	39.0	3.84e-01	75.0%	87.3%
3568856	198.1.1.1 ↗	alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2	0.55	37.0	3.87e-01	70.0%	95.6%
3595656	192.29.1.0 ↗	alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding)	0.55	48.0	4.42e-01	100.0%	83.0%
3755128	604.1.1.1 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin	0.53	41.0	4.23e-01	81.0%	88.4%
5046448	181.1.1.0 ↗	alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins	0.53	27.0	3.27e-01	77.0%	76.7%
3757581	604.1.1.1 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin	0.53	40.0	3.99e-01	81.0%	85.7%
3669281	109.4.1.1336 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, PPR_2, PPR_3	0.51	28.0	2.71e-01	83.0%	44.1%

D2 medium residues 40-85_139-157

PDB

Domain cluster: representative

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3nrgA00	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.63	46.0	3.24e-01	80.0%	34.1%
2kpqA01	6.10.250.730	Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces ›	0.55	40.0	3.86e-01	100.0%	67.6%
4jykA02	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.54	46.0	3.68e-01	100.0%	89.5%
3ppbA00	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.52	46.0	3.32e-01	100.0%	62.8%
3wa8B00	1.10.520.40	Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › CRISPR-associated protein Cse2	0.51	38.0	2.84e-01	81.5%	45.1%

D3 medium residues 86-138_216-270

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009337432__Changjiang_tombus-like_virus_5__1922819__D23-82_137-181

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00978.27 best	RdRP_2	36.5	3.80e-09	50.9%	12.0%
PF00978.27	RdRP_2	38.1	1.30e-09	46.3%	8.9%

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3umoA00	3.40.1190.20	Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase	0.51	38.0	2.81e-01	79.6%	97.7%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2723530	282.1.1.0 ↗	a+b duplicates or obligate multimers › CBS-domain › CBS-domain › CBS-domain	0.51	28.0	2.61e-01	90.7%	38.5%
3385443	2008.1.1.0 ↗	a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like	0.50	41.0	3.41e-01	91.7%	73.2%

D4 medium residues 158-215_271-335

PDB

Domain cluster: rep: RdRp,_partial__YP_008858531__Carnation_yellow_fleck_virus__940280__D190-234_286-374

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00978.27 best	RdRP_2	51.5	1.10e-13	54.5%	14.3%
PF00978.27	RdRP_2	63.7	2.10e-17	52.8%	13.9%