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MF614628.1__ATE84724.1__phi3LM21_p38__00038

Bact-Vir

MF614628.1__ATE84724.1__phi3LM21_p38__00038

Identity

Accession:
MF614628 ↗
Kingdom:
phage

Quality

91.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Sinorhizobium_phage_phi3LM21

TaxID: 2029634

Cluster

View cluster (351 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 4-138
PDB
Domain cluster: rep: MT764210__UXF49854.1__7841G1D8-26__00026__D257-398
CATH (53)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3fz2A00 3.30.70.1700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Phage minor tail protein U 0.85 75.0 7.75e-01 99.3% 98.4%
6toaF01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.82 75.0 7.70e-01 98.5% 100.0%
2gjvA00 3.30.2000.10 Alpha Beta › 2-Layer Sandwich › STM4215-like › Phage tail protein-like 0.81 73.0 7.35e-01 100.0% 95.6%
4hudA01 3.30.2000.40 Alpha Beta › 2-Layer Sandwich › STM4215-like › Myoviridae tail sheath stabiliser 0.78 74.0 6.24e-01 100.0% 81.0%
2rjzA02 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.72 50.0 5.74e-01 99.3% 98.0%
2l25A00 3.30.2000.20 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.71 66.0 6.55e-01 100.0% 96.5%
2y3uA02 3.30.980.50 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › 0.70 51.0 5.49e-01 100.0% 90.3%
6ue9L02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 42.0 4.43e-01 74.8% 67.2%
5xoyB02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 42.0 4.63e-01 82.2% 76.6%
4q7aC02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 42.0 4.65e-01 91.9% 76.9%
2nyiA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.68 39.0 4.58e-01 82.2% 83.3%
2lfpA01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.67 59.0 5.91e-01 98.5% 94.1%
3njcA00 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.65 43.0 4.16e-01 97.0% 58.8%
3pcoB06 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.65 39.0 4.59e-01 95.6% 86.2%
1b7yB06 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.64 35.0 4.23e-01 74.1% 81.4%
4iyqA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 42.0 4.62e-01 91.9% 83.2%
3ct9A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 39.0 4.35e-01 83.7% 76.6%
2vqeE01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.64 26.0 3.48e-01 85.2% 71.9%
4e98C00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 41.0 4.62e-01 91.9% 84.8%
2zomA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 41.0 4.56e-01 91.9% 83.2%
5k8mA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 44.0 4.50e-01 89.6% 74.0%
4y6iA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 41.0 4.61e-01 88.9% 86.4%
2nuhA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 41.0 4.59e-01 88.9% 85.6%
3ahpA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 41.0 4.51e-01 88.9% 84.0%
2f7vA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 41.0 4.46e-01 90.4% 83.3%
1hc7A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.61 54.0 4.36e-01 98.5% 82.9%
3l4gC04 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.61 56.0 4.40e-01 100.0% 94.2%
7by6B04 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.61 55.0 4.57e-01 97.8% 99.1%
3l4gB04 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.61 55.0 4.82e-01 98.5% 100.0%
2bkyX00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.61 37.0 4.57e-01 94.1% 96.5%
4za1C00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 35.0 4.01e-01 83.7% 80.4%
2cjaA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.60 54.0 4.10e-01 100.0% 85.8%
5t8uB01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.60 48.0 3.83e-01 83.7% 77.0%
2xzmE01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 31.0 3.29e-01 91.1% 55.2%
1httA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 53.0 4.23e-01 98.5% 90.3%
6dw1A00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.58 52.0 4.49e-01 98.5% 81.4%
6d6tA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.58 52.0 4.48e-01 98.5% 79.5%
4afhE00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.57 51.0 4.41e-01 98.5% 78.8%
3jafA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.57 51.0 4.40e-01 98.5% 80.6%
3lvtA03 2.60.40.2210 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 38.0 3.89e-01 93.3% 71.3%
1ekrA00 3.30.70.640 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Molybdopterin cofactor biosynthesis C (MoaC) domain 0.56 44.0 4.34e-01 91.1% 78.3%
1vm0A00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.56 36.0 4.16e-01 97.8% 92.5%
4frwA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 38.0 4.50e-01 73.3% 100.0%
3otlA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.55 39.0 3.75e-01 73.3% 88.2%
4azsA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 33.0 3.93e-01 98.5% 98.8%
3byqA00 3.30.1330.110 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › BB2672 0.53 43.0 3.86e-01 86.7% 88.5%
4epaA00 2.40.170.20 Mainly Beta › Beta Barrel › Maltoporin; Chain A › TonB-dependent receptor, beta-barrel domain 0.53 39.0 2.56e-01 77.0% 78.3%
1omsA00 3.30.70.1050 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Trigger factor ribosome-binding domain 0.52 36.0 3.91e-01 71.1% 100.0%
3qfgA00 2.60.40.1240 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 41.0 4.00e-01 88.1% 77.2%
3nrfA00 2.60.40.4110 Mainly Beta › Sandwich › Immunoglobulin-like › Protein of unknown function DUF4354 0.52 33.0 3.73e-01 85.9% 85.3%
3qw9B00 2.60.40.4100 Mainly Beta › Sandwich › Immunoglobulin-like › Zona pellucida, ZP-C domain 0.52 43.0 4.01e-01 87.4% 98.8%
3o6qA02 3.30.70.2720 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 36.0 3.92e-01 73.3% 93.9%
3go9A02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.51 44.0 3.74e-01 93.3% 79.3%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3966645 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.83 73.0 7.61e-01 97.0% 99.2%
4928893 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.83 79.0 7.68e-01 99.3% 97.9%
5083619 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.82 77.0 7.56e-01 99.3% 98.6%
364035 304.124.1.1 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_U 0.82 75.0 7.56e-01 99.3% 97.7%
4034134 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.82 71.0 7.37e-01 97.0% 98.4%
5040945 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.82 78.0 7.48e-01 100.0% 95.3%
2642577 304.124.1.3 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › DUF3168 0.82 76.0 7.64e-01 99.3% 97.8%
5454 304.124.1.2 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Gp37 0.81 73.0 7.39e-01 100.0% 97.0%
5083880 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.80 75.0 7.32e-01 100.0% 100.0%
4030972 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.78 66.0 7.02e-01 99.3% 100.0%
4034595 304.124.1.0 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.78 66.0 6.95e-01 97.8% 100.0%
4883824 304.124.1.6 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › DUF5072 0.78 66.0 6.80e-01 100.0% 93.8%
4291659 304.124.1.8 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_Mu_Gp37 0.77 72.0 7.14e-01 98.5% 97.9%
3970985 304.124.1.9 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_terminator_9 0.74 69.0 6.80e-01 100.0% 99.3%
3949263 304.124.1.9 ↗ a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_terminator_9 0.73 55.0 6.18e-01 89.6% 100.0%
4562028 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.69 52.0 5.16e-01 99.3% 73.8%
4069303 304.153.1.1 ↗ a+b two layers › Alpha-beta plaits › Collagenase G catalytic helper subdomain › Collagenase G catalytic helper subdomain › ColG_sub 0.69 51.0 5.37e-01 100.0% 85.8%
3972051 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.69 46.0 4.69e-01 89.6% 69.2%
4976864 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.66 50.0 4.70e-01 100.0% 66.3%
5024124 304.15.1.0 ↗ a+b two layers › Alpha-beta plaits › Viral DNA-binding domain › Viral DNA-binding domain 0.66 35.0 4.39e-01 83.0% 86.3%
3218984 304.18.1.0 ↗ a+b two layers › Alpha-beta plaits › Anticodon-binding domain of PheRS › Anticodon-binding domain of PheRS 0.64 42.0 4.45e-01 91.1% 75.0%
4937678 314.1.1.3 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.64 58.0 4.25e-01 100.0% 71.1%
4941737 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.63 56.0 4.86e-01 97.0% 100.0%
3696144 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.62 57.0 3.37e-01 99.3% 31.4%
409322 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.62 41.0 4.48e-01 91.9% 83.2%
None — 0.62 56.0 3.81e-01 100.0% 52.7%
None — 0.61 56.0 3.80e-01 100.0% 52.2%
4021057 314.1.1.0 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.61 56.0 4.41e-01 100.0% 98.5%
4932334 314.1.1.3 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.61 56.0 3.76e-01 100.0% 50.2%
None — 0.61 56.0 3.77e-01 100.0% 51.7%
3583468 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.61 40.0 4.42e-01 91.9% 81.8%
3588477 304.31.1.1 ↗ a+b two layers › Alpha-beta plaits › HMG-CoA reductase › NAD-binding domain of HMG-CoA reductase › HMG-CoA_red 0.60 42.0 4.59e-01 91.1% 88.2%
4325103 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.60 52.0 4.40e-01 94.1% 87.7%
3207181 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.59 35.0 4.14e-01 100.0% 86.7%
4360648 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.59 53.0 4.56e-01 97.0% 93.3%
3839688 872.10.1.0 ↗ a+b two layers › Dodecin subunit-like › Secreted protein HP1454 N-terminal domain › Secreted protein HP1454 N-terminal domain 0.59 37.0 4.37e-01 77.8% 94.4%
4970549 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.57 44.0 4.42e-01 82.2% 79.3%
3588078 872.3.1.0 ↗ a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like 0.57 37.0 4.42e-01 89.6% 98.9%
3213160 11.12.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.57 52.0 4.65e-01 100.0% 84.9%
3734507 331.10.1.1 ↗ a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › S-adenosylmethionine decarboxylase › SAM_decarbox 0.56 43.0 3.07e-01 79.3% 96.4%
3723425 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.56 44.0 3.28e-01 82.2% 44.9%
1312442 12.1.1.43 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Glyco_hydro_38 0.56 39.0 4.20e-01 95.6% 84.5%
4124402 7503.1.1.17 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › PF26521 0.55 41.0 4.07e-01 78.5% 96.6%
4978221 304.102.1.2 ↗ a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › TruD 0.55 47.0 4.03e-01 91.1% 93.3%
3806477 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.55 49.0 4.55e-01 98.5% 89.4%
3941539 1.1.13.40 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_min_tail 0.54 40.0 4.48e-01 89.6% 99.0%
3470249 304.42.1.0 ↗ a+b two layers › Alpha-beta plaits › Molybdenum cofactor biosynthesis protein C, MoaC › Molybdenum cofactor biosynthesis protein C, MoaC 0.54 45.0 4.44e-01 91.1% 83.4%
5054179 304.42.1.1 ↗ a+b two layers › Alpha-beta plaits › Molybdenum cofactor biosynthesis protein C, MoaC › Molybdenum cofactor biosynthesis protein C, MoaC › MoaC 0.53 43.0 4.24e-01 88.1% 80.0%
4950751 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.53 41.0 4.09e-01 91.1% 78.6%
3642420 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.53 48.0 4.67e-01 100.0% 98.7%
4338725 306.7.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.53 37.0 3.99e-01 71.1% 99.1%
3720613 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.53 41.0 2.91e-01 80.7% 38.7%
3970688 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 33.0 3.76e-01 87.4% 87.0%
3353115 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 47.0 3.73e-01 99.3% 58.8%
3495018 11.12.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like 0.51 45.0 3.91e-01 100.0% 76.4%
3332951 206.1.1.72 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, Pkinase_fungal 0.50 46.0 3.37e-01 100.0% 42.9%