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Ribonucleoside-diphosphate_reductase

Euk-Vir

Pandoravirus_dulcis

Ribonucleoside-diphosphate_reductase__YP_008319822__Pandoravirus_dulcis__1349409

Identity

Accession:: YP_008319822 ↗
Protein ID:: Ribonucleoside-diphosphate_reductase
Kingdom:: euk

Quality

76.7 mean pLDDT

Cluster

View cluster (6 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 967-1131_1173-1217_1302-1314

PDB

Domain cluster: rep: rr1__YP_009552690__Operophtera_brumata_nucleopolyhedrovirus__1046267__D445-618_684-706

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02867.21 best	Ribonuc_red_lgC	185.5	2.30e-54	95.1%	34.2%

D2 medium residues 48-238

PDB

Domain cluster: rep: Ribonucleoside-diphosphate_reductase__YP_009481447__Pandoravirus_macleodensis__2107707__D43-225

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00317.27 best	Ribonuc_red_lgN	42.1	1.10e-10	31.9%	76.6%

D3 medium residues 239-331_823-839

PDB

Domain cluster: rep: MW074125.1__QXO06237.1__X__00148__D220-303

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02867.21 best	Ribonuc_red_lgC	115.4	4.10e-33	82.7%	17.6%

D4 medium residues 332-358_376-411_793-822

PDB

Domain cluster: representative

CATH (10)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4o1sA00	2.170.16.10	Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain	0.87	80.0	6.35e-01	96.8%	97.1%
1am2A00	2.170.16.10	Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain	0.82	75.0	5.82e-01	95.7%	98.9%
1zdeA00	2.170.16.10	Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain	0.77	71.0	5.77e-01	97.8%	93.8%
6vgwA01	2.170.16.10	Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain	0.75	69.0	5.92e-01	98.9%	100.0%
2lwyA00	2.170.16.10	Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain	0.69	61.0	5.33e-01	95.7%	97.1%
3fe4B00	3.10.200.10	Alpha Beta › Roll › Carbonic Anhydrase II › Alpha carbonic anhydrase	0.60	51.0	3.79e-01	93.5%	64.5%
4lx3A00	2.170.16.10	Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain	0.58	51.0	4.93e-01	92.5%	95.0%
2f91A02	2.40.10.10	Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases	0.57	48.0	4.50e-01	92.5%	93.8%
1zs7A01	3.10.450.120	Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Pre-PUA domain; domain 1	0.55	38.0	3.66e-01	71.0%	69.2%
2lt1A00	2.40.10.170	Mainly Beta › Beta Barrel › Thrombin, subunit H ›	0.54	36.0	3.90e-01	83.9%	85.3%

ECOD (30)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3026658	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.88	79.0	6.42e-01	94.6%	98.7%
4392318	69.1.1.4 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing	0.88	79.0	6.09e-01	94.6%	99.5%
4948016	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.86	75.0	6.25e-01	91.4%	97.3%
4983458	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.86	77.0	6.22e-01	94.6%	98.2%
4993480	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.86	81.0	6.60e-01	100.0%	99.4%
5023539	69.1.1.4 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing	0.85	76.0	6.24e-01	94.6%	100.0%
4978263	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.85	78.0	6.28e-01	97.8%	97.0%
4335483	69.1.1.4 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing	0.84	76.0	5.56e-01	95.7%	99.6%
4322985	2004.1.1.14 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › GTP_EFTU	0.83	79.0	5.12e-01	100.0%	39.2%
4629526	69.1.1.4 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing	0.83	75.0	5.05e-01	96.8%	100.0%
4544734	69.1.1.4 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing	0.82	76.0	5.62e-01	96.8%	100.0%
4060462	69.1.1.4 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing	0.82	77.0	5.31e-01	100.0%	97.5%
3604383	69.1.1.4 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing	0.82	74.0	5.48e-01	95.7%	98.1%
4977673	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.81	74.0	5.36e-01	95.7%	99.1%
5031634	69.1.1.4 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing	0.81	74.0	6.01e-01	96.8%	95.0%
4872043	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.78	72.0	5.97e-01	96.8%	96.7%
4291841	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.77	68.0	5.56e-01	94.6%	100.0%
4992473	69.1.1.4 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Intein_splicing	0.77	71.0	5.66e-01	97.8%	92.4%
5047640	2008.1.1.0 ↗	a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like	0.62	42.0	3.54e-01	71.0%	82.4%
4779324	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.58	51.0	4.93e-01	92.5%	95.0%
3764452	4.8.1.41 ↗	beta barrels › SH3 › Chromo domain-like › Chromo domain-like › DUF4708	0.57	43.0	3.96e-01	80.6%	91.7%
4010912	223.1.1.0 ↗	a+b three layers › Profilin-like › sensor domains › sensor domains	0.55	41.0	3.70e-01	79.6%	83.1%
4319097	4.1.1.0 ↗	beta barrels › SH3 › SH3 › SH3	0.55	32.0	3.82e-01	91.4%	91.4%
3598222	4.1.1.0 ↗	beta barrels › SH3 › SH3 › SH3	0.54	34.0	3.80e-01	82.8%	85.7%
3599925	804.1.1.0 ↗	a+b four layers › Hypothetical protein YwqG › Hypothetical protein YwqG › Hypothetical protein YwqG	0.52	37.0	2.99e-01	73.1%	96.1%
5046181	2008.1.1.0 ↗	a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like	0.52	36.0	3.17e-01	74.2%	82.6%
3512351	1.1.1.0 ↗	beta barrels › cradle loop barrel › RIFT-related › acid protease	0.51	36.0	3.59e-01	93.5%	71.6%
261	1.1.17.0 ↗	beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2	0.51	42.0	3.28e-01	92.5%	93.4%
4873829	223.1.1.13 ↗	a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3	0.50	37.0	3.78e-01	81.7%	79.6%
3950403	223.1.1.2 ↗	a+b three layers › Profilin-like › sensor domains › sensor domains › PAS	0.50	38.0	3.42e-01	80.6%	77.7%

D5 medium residues 412-462_547-570_688-767

PDB

D6 medium residues 587-687

PDB

Domain cluster: rep: Ribonucleoside-diphosphate_reductase__YP_009482455__Pandoravirus_neocaledonia__2107708__D570-648

D7 medium residues 840-966_1315-1344

PDB

Domain cluster: rep: ribonucleotide-diphosphate_reductase_large_chain__YP_009119180__Pandoravirus_inopinatum__1605721__D783-936

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02867.21 best	Ribonuc_red_lgC	145.9	2.30e-42	83.4%	24.8%

D8 medium residues 1218-1301

PDB

Domain cluster: rep: IMGVR_UViG_3300006567_000026-3300006567-Ga0099958_11086953__D213-268

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02867.21 best	Ribonuc_red_lgC	51.4	1.00e-13	100.0%	15.3%