←Back to structures

MN988558.1__QIG76960.1__EVC30_132__00131

Bact-Vir

MN988558.1__QIG76960.1__EVC30_132__00131

Identity

Accession:
MN988558 ↗
Kingdom:
phage

Quality

81.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_RHph_Y1_11

TaxID: 2509770

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 high residues 10-85
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2yztA00 3.30.160.250 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.67 50.0 5.36e-01 92.1% 92.4%
1rykA00 1.10.1470.10 Mainly Alpha › Orthogonal Bundle › Protein Yjbj; Chain: A; › YjbJ 0.63 45.0 4.71e-01 76.3% 85.5%
3lhxA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.62 45.0 3.06e-01 77.6% 94.3%
4cswA02 3.40.366.30 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › 50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2 0.62 46.0 3.49e-01 78.9% 43.2%
2xdvA03 3.90.930.40 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.61 46.0 4.05e-01 78.9% 78.2%
3kcpA02 2.60.40.1120 Mainly Beta › Sandwich › Immunoglobulin-like › Carboxypeptidase-like, regulatory domain 0.60 41.0 3.79e-01 71.1% 75.8%
3eagA02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.58 43.0 3.10e-01 78.9% 30.7%
2abqA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.58 42.0 2.89e-01 78.9% 38.4%
2nt2A00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.58 43.0 3.55e-01 80.3% 86.6%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.58 42.0 4.38e-01 82.9% 88.1%
6ilsA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.58 42.0 2.85e-01 78.9% 31.1%
1whzA00 3.30.920.30 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. 0.56 39.0 4.01e-01 78.9% 81.2%
2k49A00 2.30.29.80 Mainly Beta › Roll › PH-domain like › 0.55 44.0 3.90e-01 92.1% 93.2%
3j7aF02 2.40.50.740 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Ribosomal protein S4, central domain 0.54 34.0 4.01e-01 71.1% 94.1%
1onwA01 2.30.40.10 Mainly Beta › Roll › Urease, subunit C; domain 1 › Urease, subunit C, domain 1 0.54 37.0 3.30e-01 97.4% 49.1%
3ottB02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 39.0 2.57e-01 75.0% 37.7%
4m8aA00 3.30.720.210 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.54 35.0 3.66e-01 89.5% 74.6%
4z32A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 38.0 3.60e-01 89.5% 59.4%
3nqhA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.53 39.0 2.68e-01 78.9% 85.5%
6az1E02 2.40.50.740 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Ribosomal protein S4, central domain 0.53 33.0 3.82e-01 71.1% 94.1%
2e50B02 3.30.1120.90 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › Nucleosome assembly protein 0.52 45.0 4.04e-01 100.0% 72.1%
3dsoA00 2.40.10.300 Mainly Beta › Beta Barrel › Thrombin, subunit H › Copper resistance protein K 0.52 33.0 3.56e-01 88.2% 75.8%
1ye8A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 44.0 3.52e-01 98.7% 77.2%
4bpnW02 2.40.50.740 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Ribosomal protein S4, central domain 0.52 32.0 3.74e-01 71.1% 94.1%
4amwA01 2.60.40.1760 Mainly Beta › Sandwich › Immunoglobulin-like › glycosyl hydrolase (family 31) 0.51 41.0 2.84e-01 94.7% 77.4%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4032637 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.69 37.0 4.24e-01 86.8% 70.9%
5062937 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.69 48.0 4.23e-01 72.4% 94.5%
2512682 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.68 39.0 4.44e-01 89.5% 78.2%
3990001 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.67 37.0 4.29e-01 86.8% 75.5%
4964361 502.1.1.3 ↗ a+b two layers › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain › DUF7348 0.64 42.0 4.36e-01 84.2% 71.4%
4960839 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 46.0 4.27e-01 77.6% 87.0%
3953675 330.7.1.0 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain 0.61 43.0 4.54e-01 81.6% 86.2%
4072958 2.1.1.9 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_S4e 0.61 43.0 4.61e-01 73.7% 86.2%
5055849 330.7.1.2 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › HicA_toxin 0.59 40.0 4.22e-01 76.3% 81.5%
5011606 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.59 49.0 3.71e-01 92.1% 81.4%
5075725 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 48.0 3.88e-01 89.5% 93.1%
4961801 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.58 51.0 3.81e-01 100.0% 66.3%
3981692 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.58 42.0 2.87e-01 78.9% 46.6%
5001380 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 43.0 4.30e-01 80.3% 93.8%
5075755 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.58 49.0 3.92e-01 96.1% 91.3%
3511321 5.1.4.298 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_ELP1_1st, Beta-prop_ELP1_2nd 0.58 42.0 2.50e-01 77.6% 12.7%
3603682 2484.1.1.211 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605, Cas12f1-like_TNB 0.58 50.0 3.60e-01 97.4% 60.9%
5013223 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.58 46.0 3.37e-01 86.8% 63.4%
3915890 10.1.1.5 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Pentaxin 0.57 42.0 3.72e-01 77.6% 78.2%
3675412 386.1.1.6 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › ARS2 0.57 37.0 3.70e-01 80.3% 63.7%
4977784 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.57 49.0 3.47e-01 96.1% 67.2%
5005258 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.57 48.0 3.61e-01 97.4% 73.2%
4043931 2.1.1.9 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_S4e 0.56 39.0 4.32e-01 77.6% 91.7%
3272708 292.2.1.1 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › POLO_box 0.56 45.0 4.51e-01 88.2% 88.7%
3773509 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.56 35.0 3.85e-01 75.0% 80.0%
4023063 216.1.1.8 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › Knl1_RWD_C 0.56 41.0 3.86e-01 78.9% 98.9%
4994780 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.55 47.0 3.45e-01 96.1% 66.0%
4957480 5.1.4.40 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PQQ_2 0.55 43.0 2.78e-01 85.5% 46.6%
5079107 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 46.0 3.83e-01 90.8% 82.3%
4944767 101.1.2.883 ↗ alpha arrays › HTH › HTH › winged helix domain › Radical_SAM 0.55 40.0 4.08e-01 82.9% 80.0%
4279317 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.54 42.0 2.64e-01 86.8% 68.6%
5008972 2005.1.1.17 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1f 0.54 42.0 2.64e-01 86.8% 68.6%
4945986 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.54 45.0 3.35e-01 96.1% 74.9%
3819067 386.1.1.207 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-BED_2 0.53 41.0 4.36e-01 88.2% 98.5%
4626529 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.53 42.0 2.90e-01 92.1% 93.9%
3891866 220.1.1.49 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Carm_PH 0.52 38.0 3.21e-01 89.5% 42.9%
3451441 220.1.1.29 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_3 0.52 44.0 3.86e-01 100.0% 95.1%
4929228 220.1.1.87 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_3 0.51 41.0 3.83e-01 90.8% 81.8%
3566576 220.1.1.49 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Carm_PH 0.51 43.0 3.45e-01 96.1% 48.1%
5024071 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 41.0 3.73e-01 96.1% 82.6%
3998283 3534.1.1.3 ↗ beta barrels › Pfam PF06938 (DUF1285) › Pfam PF06938 (DUF1285) › Pfam PF06938 (DUF1285) › DUF4505 0.50 35.0 3.47e-01 89.5% 67.1%
3874132 220.1.1.170 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_alsin 0.50 39.0 3.40e-01 89.5% 54.8%