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ribonucleoside-diphosphate_reductase_large_subunit
Euk-VirPithovirus_sibericum
ribonucleoside-diphosphate_reductase_large_subunit__YP_009001024__Pithovirus_sibericum__1450746
Identity
- Accession:
- YP_009001024 ↗
- Protein ID:
- ribonucleoside-diphosphate_reductase_large_subunit
- Kingdom:
- euk
Quality
91.8
mean pLDDT
Cluster
View cluster (122 members)3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 181-398_746-776
Domain cluster:
rep: IMGVR_UViG_3300042092_000730-3300042092-Ga0453238_010587_859_2079__D220-402
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02867.21 best | Ribonuc_red_lgC | 205.3 | 2.30e-60 | 88.3% | 42.4% |
D2
medium
residues 2-54
Domain cluster:
representative
CATH (21)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3vw5A00 | 1.50.10.10 | Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › | 0.72 | 57.0 | 3.36e-01 | 84.9% | 16.5% |
| 5n17A01 | 1.20.920.10 | Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like | 0.71 | 60.0 | 4.94e-01 | 100.0% | 88.5% |
| 2wj9B00 | 3.30.70.3580 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Antirestriction protein | 0.70 | 59.0 | 4.41e-01 | 100.0% | 92.4% |
| 4n4gA01 | 1.20.920.10 | Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like | 0.69 | 59.0 | 4.71e-01 | 100.0% | 75.7% |
| 2rbdA01 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.66 | 51.0 | 3.78e-01 | 88.7% | 90.0% |
| 3lcnB00 | 1.10.340.40 | Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain | 0.64 | 51.0 | 4.24e-01 | 88.7% | 58.8% |
| 2ntxA01 | 1.20.58.2010 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › PRONE domain, subdomain 1 | 0.63 | 52.0 | 3.52e-01 | 96.2% | 72.4% |
| 4z4qA04 | 1.10.268.10 | Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 | 0.63 | 48.0 | 4.14e-01 | 86.8% | 53.9% |
| 1elkA00 | 1.25.40.90 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.61 | 46.0 | 3.40e-01 | 84.9% | 41.8% |
| 3bjdA01 | 1.10.1240.20 | Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Lytic transglycosylase, superhelical linker domain | 0.60 | 44.0 | 3.86e-01 | 83.0% | 85.2% |
| 2db0B00 | 1.25.10.10 | Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant | 0.60 | 49.0 | 3.22e-01 | 94.3% | 34.6% |
| 1kz7A01 | 1.20.900.10 | Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain | 0.59 | 49.0 | 3.44e-01 | 100.0% | 62.7% |
| 1o0sA02 | 1.20.1370.30 | Mainly Alpha › Up-down Bundle › Hemocyanin, N-terminal domain › | 0.57 | 42.0 | 3.53e-01 | 86.8% | 50.9% |
| 1dt9A01 | 3.30.960.10 | Alpha Beta › 2-Layer Sandwich › Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A › eRF1 domain 1 | 0.56 | 45.0 | 3.73e-01 | 94.3% | 55.2% |
| 1uaaA02 | 1.10.10.160 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › | 0.56 | 45.0 | 4.18e-01 | 100.0% | 90.5% |
| 3uo2B02 | 1.20.1280.20 | Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain | 0.56 | 41.0 | 3.63e-01 | 83.0% | 84.5% |
| 3qqaA02 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.55 | 41.0 | 3.20e-01 | 86.8% | 58.2% |
| 2jqtA00 | 1.20.1280.40 | Mainly Alpha › Up-down Bundle › Monooxygenase › HHA | 0.54 | 42.0 | 4.16e-01 | 88.7% | 89.5% |
| 7ckaA01 | 1.20.910.10 | Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like | 0.53 | 44.0 | 3.09e-01 | 98.1% | 55.4% |
| 4mlmA00 | 1.10.3210.10 | Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 | 0.52 | 43.0 | 3.05e-01 | 100.0% | 39.9% |
| 4dmvA01 | 1.20.58.1190 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.52 | 40.0 | 3.64e-01 | 96.2% | 98.8% |
ECOD (14)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4862607 | 633.16.1.2 ↗ | alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like › TcdB_N | 0.68 | 58.0 | 4.97e-01 | 100.0% | 84.3% |
| 4027904 | 174.1.1.0 ↗ | few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain | 0.68 | 58.0 | 4.65e-01 | 100.0% | 94.5% |
| 4032823 | 603.1.1.0 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins | 0.65 | 52.0 | 4.51e-01 | 86.8% | 88.7% |
| 4929738 | 6049.1.1.0 ↗ | alpha bundles › PH0832-like › PH0832-like › PH0832-like | 0.65 | 53.0 | 4.86e-01 | 98.1% | 84.0% |
| 3476348 | 611.3.1.2 ↗ | alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › LEDGF | 0.64 | 50.0 | 3.83e-01 | 86.8% | 46.4% |
| 3801107 | 626.1.1.1 ↗ | alpha complex topology › Formin homology 2 domain (FH2 domain) › Formin homology 2 domain (FH2 domain) › Formin homology 2 domain (FH2 domain) › FH2 | 0.64 | 50.0 | 2.98e-01 | 88.7% | 53.3% |
| 5034860 | 2004.1.1.94 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATP_bind_1 | 0.63 | 47.0 | 3.08e-01 | 84.9% | 31.8% |
| 4929122 | 7000.1.1.0 ↗ | alpha arrays › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS | 0.62 | 49.0 | 4.66e-01 | 88.7% | 72.3% |
| 3227370 | 109.4.1.17 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cullin | 0.60 | 44.0 | 3.54e-01 | 84.9% | 80.0% |
| 3583980 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.59 | 43.0 | 3.56e-01 | 83.0% | 85.7% |
| 3918791 | 150.3.1.0 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine | 0.58 | 45.0 | 3.32e-01 | 90.6% | 67.1% |
| 5066260 | 2004.1.1.94 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATP_bind_1 | 0.57 | 42.0 | 2.82e-01 | 84.9% | 30.8% |
| 4032384 | 604.3.1.0 ↗ | alpha bundles › Spectrin repeat-like › BAG domain › BAG domain | 0.57 | 42.0 | 3.83e-01 | 86.8% | 86.3% |
| 4169083 | 7579.1.1.10 ↗ | a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Thioesterase | 0.55 | 43.0 | 2.79e-01 | 92.5% | 17.9% |
D3
medium
residues 159-177_405-510_613-645_728-745_825-836
Domain cluster:
rep: rr1__YP_009552690__Operophtera_brumata_nucleopolyhedrovirus__1046267__D445-618_684-706
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02867.21 best | Ribonuc_red_lgC | 82.1 | 5.10e-23 | 60.6% | 19.3% |
| PF02867.21 | Ribonuc_red_lgC | 26.5 | 3.50e-06 | 21.8% | 6.7% |
D4
medium
residues 646-727
Domain cluster:
representative
CATH (8)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3gdeA01 | 1.10.3260.10 | Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain | 0.59 | 45.0 | 3.38e-01 | 84.1% | 48.7% |
| 1u9lB00 | 1.10.150.20 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain | 0.55 | 43.0 | 4.55e-01 | 97.6% | 100.0% |
| 1x40A00 | 1.10.150.50 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 | 0.54 | 43.0 | 4.20e-01 | 98.8% | 80.2% |
| 2rrdA00 | 1.10.150.80 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › HRDC domain | 0.52 | 44.0 | 4.20e-01 | 100.0% | 87.1% |
| 5c8gB00 | 1.20.920.10 | Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like | 0.52 | 42.0 | 3.82e-01 | 90.2% | 93.2% |
| 1kv9A02 | 1.10.760.10 | Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain | 0.52 | 37.0 | 3.52e-01 | 76.8% | 72.8% |
| 2cqnA00 | 1.10.10.440 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain | 0.51 | 35.0 | 3.64e-01 | 72.0% | 77.9% |
| 1i1rB00 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.51 | 39.0 | 3.15e-01 | 82.9% | 68.3% |
ECOD (4)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3446679 | 102.5.1.0 ↗ | alpha arrays › HhH/H2TH › SAM-like subdomain in Sec63-like proteins › SAM-like subdomain in Sec63-like proteins | 0.56 | 39.0 | 4.28e-01 | 84.1% | 100.0% |
| 3335755 | 102.5.1.0 ↗ | alpha arrays › HhH/H2TH › SAM-like subdomain in Sec63-like proteins › SAM-like subdomain in Sec63-like proteins | 0.56 | 39.0 | 4.29e-01 | 84.1% | 100.0% |
| 3977009 | 101.1.3.0 ↗ | alpha arrays › HTH › HTH › tetra-helical, LuxR-like | 0.54 | 33.0 | 3.51e-01 | 81.7% | 68.6% |
| 4270690 | 101.1.3.0 ↗ | alpha arrays › HTH › HTH › tetra-helical, LuxR-like | 0.54 | 32.0 | 3.58e-01 | 81.7% | 78.3% |