←Back to structures

ribonucleotide_reductase_1

Euk-Vir

Diatraea_saccharalis_granulovirus

ribonucleotide_reductase_1__YP_009182313__Diatraea_saccharalis_granulovirus__1675862

Identity

Accession:: YP_009182313 ↗
Protein ID:: ribonucleotide_reductase_1
Kingdom:: euk

Quality

86.1 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Betabaculovirus› Diatraea_saccharalis_granulovirus

TaxID: 1675862

Cluster

View cluster (22 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 33-86

PDB

Domain cluster: representative

CATH (11)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4muoA01	1.20.970.10	Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C	0.60	41.0	3.82e-01	72.2%	56.9%
8a9nA01	3.40.630.30	Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT)	0.59	46.0	3.67e-01	96.3%	95.4%
4jrrB00	3.40.30.10	Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin	0.55	42.0	3.01e-01	87.0%	43.5%
3b0xA01	1.10.150.110	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like	0.55	43.0	3.74e-01	87.0%	89.7%
1vquA01	1.20.970.10	Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C	0.55	37.0	3.57e-01	72.2%	61.2%
2elcA01	1.20.970.10	Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C	0.55	38.0	3.60e-01	74.1%	61.2%
1zvwA01	1.20.970.10	Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C	0.54	38.0	3.60e-01	74.1%	63.6%
4mvfA03	1.10.238.10	Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand	0.54	41.0	2.98e-01	87.0%	57.5%
3waeA02	3.40.190.10	Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II	0.52	40.0	2.98e-01	88.9%	71.1%
2n1rA00	1.10.150.90	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Immunodeficiency lentiviruses, gag gene matrix protein p17	0.51	43.0	3.28e-01	98.1%	63.4%
1zv1A00	1.10.8.10	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain	0.50	34.0	3.35e-01	72.2%	72.9%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3277072	1074.1.1.1 ↗	alpha arrays › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases › Ribonuc_red_lgN	0.83	67.0	4.77e-01	88.9%	31.0%
4976420	1074.1.1.0 ↗	alpha arrays › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases	0.81	68.0	5.42e-01	92.6%	56.2%
3594035	1074.1.1.0 ↗	alpha arrays › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases	0.81	68.0	5.13e-01	94.4%	39.2%
4986026	378.1.1.2 ↗	few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH	0.76	59.0	4.00e-01	83.3%	68.6%
2983780	184.1.1.0 ↗	alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N	0.61	42.0	3.81e-01	72.2%	55.4%
1514597	184.1.1.1 ↗	alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N	0.60	41.0	3.80e-01	72.2%	56.2%
5072866	102.1.1.30 ↗	alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HHH_8	0.57	44.0	3.93e-01	88.9%	96.5%
3956445	102.1.1.30 ↗	alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HHH_8	0.55	44.0	3.81e-01	92.6%	92.2%
4003656	5048.1.1.1 ↗	alpha complex topology › Aquaporin-like › Aquaporin-like › Aquaporin-like › MIP	0.54	36.0	2.59e-01	70.4%	81.7%
4390167	184.1.1.1 ↗	alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N	0.54	37.0	3.59e-01	74.1%	63.1%
4951200	102.1.1.30 ↗	alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HHH_8	0.51	37.0	3.33e-01	83.3%	90.6%

D2 medium residues 183-251

PDB

Domain cluster: rep: IMGVR_UViG_3300007266_000133-3300007266-Ga0101450_1063125__D8-101

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02867.21 best	Ribonuc_red_lgC	26.4	3.70e-06	100.0%	12.8%

CATH (3)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2wghA00	3.20.70.20	Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain ›	0.89	83.0	4.65e-01	100.0%	10.6%
1ux5A01	6.10.30.50	Special › Helix non-globular › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 ›	0.52	28.0	2.97e-01	79.7%	60.0%
1yukA01	3.30.1680.10	Alpha Beta › 2-Layer Sandwich › ligand-binding face of the semaphorins, domain 2 › ligand-binding face of the semaphorins, domain 2	0.52	35.0	3.70e-01	79.7%	84.7%

ECOD (9)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3823652	2500.1.1.2 ↗	a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC	0.90	84.0	4.77e-01	100.0%	12.0%
4822330	2500.1.1.2 ↗	a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC	0.89	85.0	4.96e-01	100.0%	15.3%
4015532	2500.1.1.0 ↗	a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel	0.89	83.0	4.73e-01	100.0%	11.8%
5079449	2004.1.1.97 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MobB	0.62	42.0	3.23e-01	72.5%	91.2%
3794363	282.1.1.0 ↗	a+b duplicates or obligate multimers › CBS-domain › CBS-domain › CBS-domain	0.61	44.0	4.13e-01	95.7%	62.4%
3410469	304.20.1.3 ↗	a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › Nrap_D6	0.55	41.0	3.36e-01	82.6%	97.9%
3728468	327.5.1.7 ↗	a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › Mug62	0.53	42.0	3.23e-01	87.0%	70.3%
4976722	2485.1.1.0 ↗	a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like	0.53	36.0	3.24e-01	72.5%	75.2%
3786451	327.5.1.7 ↗	a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › Mug62	0.52	42.0	3.16e-01	89.9%	72.8%

D3 medium residues 302-549

PDB

Domain cluster: rep: rr1__YP_009553415__Tomelloso_virus__2053981__D128-178_338-351_396-661_674-684

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02867.21 best	Ribonuc_red_lgC	59.2	4.50e-16	78.2%	40.6%