←Back to structures

YqaJ-like_viral_recombinase

Euk-Vir

Mollivirus_sibericum_Viruses.

YqaJ-like_viral_recombinase__YP_009165300__Mollivirus_sibericum_Viruses.__X

Identity

Accession:
YP_009165300 ↗
Protein ID:
YqaJ-like_viral_recombinase
Kingdom:
euk

Quality

56.3 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 35-103
PDB
D2 medium residues 104-223
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3syyA00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.83 74.0 6.10e-01 100.0% 57.2%
3sm4A00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.78 70.0 5.55e-01 100.0% 50.7%
4ic1D00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.77 65.0 5.34e-01 100.0% 51.9%
4dunA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.70 38.0 3.81e-01 99.2% 51.2%
1i74A02 3.10.310.20 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › DHHA2 domain 0.67 44.0 4.51e-01 100.0% 68.1%
8d3mI01 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.65 60.0 4.91e-01 100.0% 57.0%
4hjhA02 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.64 40.0 4.66e-01 97.5% 91.4%
1u0kA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.64 36.0 3.56e-01 99.2% 50.8%
6upsA01 3.40.395.10 Alpha Beta › 3-Layer(aba) Sandwich › Adenoviral Proteinase; Chain › Adenoviral Proteinase; Chain A 0.62 38.0 3.54e-01 96.7% 47.7%
2fkcA01 3.40.1350.40 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.62 49.0 5.11e-01 96.7% 91.8%
1p5dX02 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.61 37.0 4.37e-01 94.2% 91.0%
2w8mA00 3.40.1350.50 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › D212 PD-(D/E)XK nuclease, catalytic motif 0.59 53.0 4.76e-01 100.0% 70.9%
1qy9A02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.59 44.0 3.97e-01 78.3% 59.5%
4lqeA00 3.40.1350.140 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › MepB-like 0.58 45.0 4.21e-01 95.0% 65.8%
4ciuA04 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.58 33.0 3.67e-01 99.2% 71.0%
3ndhA00 3.40.600.30 Alpha Beta › 3-Layer(aba) Sandwich › ECO RV Endonuclease; Chain A › 0.57 46.0 3.81e-01 100.0% 48.1%
3kxwA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.57 42.0 4.20e-01 76.7% 93.5%
2ezvA01 3.40.600.40 Alpha Beta › 3-Layer(aba) Sandwich › ECO RV Endonuclease; Chain A › Type II restriction enzyme SfiI, multifunctional domain 0.57 49.0 4.09e-01 100.0% 55.3%
4ls9B02 3.10.310.30 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › 0.56 39.0 3.95e-01 71.7% 72.4%
2rqlA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.56 35.0 3.84e-01 96.7% 76.8%
4b08A01 2.40.50.730 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 33.0 3.99e-01 81.7% 88.9%
1cqmA00 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.55 36.0 3.94e-01 81.7% 80.6%
1atnD00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.54 50.0 3.86e-01 100.0% 70.5%
2xi5A00 3.40.91.60 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › 0.52 46.0 4.05e-01 100.0% 65.2%
2b9eA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 44.0 3.77e-01 95.8% 100.0%
2vqeL00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 36.0 3.62e-01 78.3% 71.8%
3r1kA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.50 44.0 4.33e-01 97.5% 88.0%
1ym3A00 3.40.1050.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-carbonic Anhydrase; Chain A › Carbonic anhydrase 0.50 45.0 3.83e-01 97.5% 77.2%
ECOD (68)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
222168 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.77 65.0 5.34e-01 100.0% 51.9%
3927949 2008.1.1.29 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Dna2 0.76 71.0 5.61e-01 100.0% 76.6%
5080739 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.76 71.0 5.57e-01 100.0% 68.5%
5039697 2008.1.1.224 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_3 0.75 57.0 5.81e-01 98.3% 80.7%
4932253 2008.1.1.100 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › HSDR_N_2 0.74 62.0 5.79e-01 98.3% 73.1%
5023848 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.74 43.0 4.26e-01 75.8% 53.8%
5038690 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.74 68.0 6.12e-01 99.2% 75.6%
3594135 2008.2.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.73 58.0 6.31e-01 94.2% 100.0%
4942551 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.73 64.0 5.20e-01 100.0% 51.8%
4324924 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.73 65.0 5.81e-01 95.8% 80.6%
3172160 2008.1.1.29 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Dna2 0.71 66.0 5.23e-01 100.0% 78.3%
3414564 2008.1.1.29 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Dna2 0.71 66.0 4.89e-01 100.0% 61.8%
4152182 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.70 51.0 5.66e-01 100.0% 96.8%
3744035 2008.1.1.29 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Dna2 0.69 64.0 4.90e-01 100.0% 66.0%
4046575 286.1.1.2 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › PhzC-PhzF 0.68 38.0 3.94e-01 71.7% 56.5%
4936990 5104.1.1.3 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA2 0.68 45.0 4.58e-01 98.3% 68.6%
3249997 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.67 55.0 4.83e-01 100.0% 59.2%
11031 2008.1.1.40 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Endonuc-MspI 0.66 60.0 4.65e-01 100.0% 76.3%
5012280 2008.1.1.59 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.65 59.0 4.87e-01 100.0% 56.6%
3515746 2008.1.1.91 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NARG2_C 0.65 46.0 4.20e-01 73.3% 60.6%
4242672 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.65 60.0 5.01e-01 100.0% 66.0%
4494448 2008.1.1.183 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF27227 0.65 58.0 5.59e-01 96.7% 86.7%
3980839 2008.1.1.77 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NOV_C 0.65 56.0 5.19e-01 98.3% 73.9%
2985793 2008.1.1.4 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Cas_Cas4 0.65 60.0 4.82e-01 100.0% 54.1%
3543559 2008.2.1.3 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › SLFN_GTPase-like 0.64 59.0 5.41e-01 99.2% 78.7%
4622034 327.7.1.9 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › SLFN_GTPase-like 0.64 59.0 5.22e-01 99.2% 71.5%
3732342 7502.1.1.2 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Brix 0.63 39.0 3.07e-01 100.0% 29.8%
3989767 2008.1.1.152 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF2130 0.63 57.0 4.97e-01 100.0% 65.6%
4352045 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.62 35.0 3.93e-01 97.5% 71.1%
4486867 3351.1.1.0 ↗ a/b three-layered sandwiches › Atg7 N-terminal domain-like › N-terminal domain in E1 enzyme Atg7 › N-terminal domain in E1 enzyme Atg7 0.62 43.0 4.64e-01 98.3% 85.0%
3838560 2008.1.1.78 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_endonuc 0.62 56.0 4.75e-01 99.2% 63.1%
4236550 2003.1.5.82 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.62 46.0 3.12e-01 77.5% 34.5%
5022884 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 44.0 4.53e-01 98.3% 78.3%
4642198 7502.1.1.2 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Brix 0.61 36.0 2.87e-01 100.0% 28.5%
3580762 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 50.0 3.91e-01 99.2% 41.1%
3499164 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.60 50.0 3.70e-01 100.0% 34.5%
3989509 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.60 31.0 3.22e-01 97.5% 50.9%
402316 2008.1.1.65 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › L_protein_N 0.60 52.0 4.51e-01 97.5% 61.2%
3521006 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.59 52.0 4.29e-01 95.8% 83.3%
3276755 2008.1.1.91 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NARG2_C 0.59 52.0 3.72e-01 100.0% 31.6%
3628154 2008.1.1.91 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NARG2_C 0.58 50.0 3.68e-01 100.0% 34.8%
3415033 2008.1.1.27 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAI1 0.58 52.0 3.73e-01 100.0% 35.6%
3589020 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 53.0 4.90e-01 99.2% 84.0%
3592513 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 51.0 3.73e-01 100.0% 43.5%
4096132 5104.1.1.1 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.57 40.0 4.12e-01 100.0% 75.7%
3238589 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 51.0 3.67e-01 100.0% 39.4%
3939159 2008.1.1.91 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NARG2_C 0.57 52.0 3.73e-01 100.0% 37.6%
4505973 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.57 50.0 3.86e-01 95.8% 61.2%
4013795 206.1.1.82 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › DUF7580 0.57 51.0 3.67e-01 98.3% 36.4%
4545641 2008.1.1.78 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_endonuc 0.56 49.0 4.39e-01 95.0% 73.5%
3964769 2008.1.1.78 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_endonuc 0.56 49.0 4.35e-01 97.5% 72.8%
4345388 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.56 49.0 3.87e-01 95.8% 62.9%
4054627 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.56 49.0 3.83e-01 95.8% 63.1%
3225936 2008.1.1.27 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAI1 0.56 50.0 3.73e-01 100.0% 39.4%
3967842 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.55 49.0 3.87e-01 97.5% 64.5%
4973169 7518.1.1.0 ↗ a/b three-layered sandwiches › PK C-terminal domain-like › PK C-terminal domain-like › PK C-terminal domain-like 0.55 41.0 4.49e-01 97.5% 95.0%
4486660 323.1.1.5 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.54 40.0 4.05e-01 89.2% 76.7%
4152187 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.54 47.0 4.84e-01 97.5% 99.1%
4438611 5104.1.1.1 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.54 37.0 3.80e-01 99.2% 73.0%
5051074 4143.1.1.1 ↗ a+b two layers › THUMP domain-like › THUMP domain-like › THUMP domain-like › THUMP 0.54 35.0 4.00e-01 95.8% 88.9%
5081645 7528.1.1.1 ↗ a/b three-layered sandwiches › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains › PGM_PMM_I 0.53 40.0 3.89e-01 95.0% 71.5%
3518388 247.1.1.1 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B 0.53 43.0 3.52e-01 88.3% 97.8%
3266455 2003.1.5.74 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltrans_SAM 0.52 47.0 3.37e-01 100.0% 63.8%
4078209 7503.1.1.3 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › TolB_N 0.52 44.0 4.21e-01 100.0% 77.9%
3700637 2003.1.2.7 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_2 0.52 44.0 3.17e-01 93.3% 91.3%
3899941 2003.1.5.156 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr, Methyltransf_31 0.52 47.0 3.20e-01 100.0% 94.8%
3735206 246.3.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › Exo_endo_phos 0.51 47.0 3.33e-01 100.0% 70.0%
5075312 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.50 45.0 4.06e-01 100.0% 83.9%
D3 medium residues 224-281
PDB