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MK580972.1__QBP06270.1__X__00074

Bact-Vir

MK580972.1__QBP06270.1__X__00074

Identity

Accession:
MK580972 ↗
Kingdom:
phage

Quality

93.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Menderavirus› Stenotrophomonas_phage_YB07

TaxID: 2555548

Cluster

View cluster (11 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 2-120
PDB
Domain cluster: rep: peptidyl-tRNA_hydrolase__YP_009447948__Flamingopox_virus_FGPVKD09__2059380__D17-122
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1q7sA00 3.40.1490.10 Alpha Beta › 3-Layer(aba) Sandwich › Bit1 › Bit1 0.77 70.0 7.06e-01 100.0% 97.4%
2gaxA00 3.40.1490.10 Alpha Beta › 3-Layer(aba) Sandwich › Bit1 › Bit1 0.68 64.0 6.10e-01 100.0% 96.3%
3pehA02 3.30.70.2140 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 27.0 3.96e-01 80.7% 97.7%
1ug8A00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.61 27.0 3.17e-01 81.5% 55.2%
3mwbB03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.61 36.0 3.96e-01 100.0% 72.6%
1y0hB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 39.0 4.25e-01 100.0% 83.7%
5o6uB00 3.30.70.2540 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › CRISPR-associated endoribonuclease Cas6/Csy4 0.57 38.0 3.30e-01 100.0% 44.0%
2mzsA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 35.0 3.84e-01 100.0% 74.7%
3g8qA02 3.30.70.1940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 36.0 4.25e-01 84.0% 96.2%
2yweA03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.56 34.0 3.96e-01 100.0% 86.6%
5fxdA03 3.40.462.10 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain 0.55 48.0 3.87e-01 95.0% 91.8%
1m1hA01 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.55 36.0 3.83e-01 73.9% 76.0%
6ztgA01 3.30.70.1070 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sporulation related repeat 0.55 33.0 3.94e-01 98.3% 93.3%
3k59A02 3.30.70.2250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › B family DNA polymerase, N domain, alpha/beta motif 0.54 30.0 3.85e-01 100.0% 97.0%
3gz7B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 37.0 4.01e-01 72.3% 90.8%
2joqA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.53 33.0 4.00e-01 100.0% 100.0%
2qycA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 37.0 3.99e-01 73.1% 87.3%
2gm3A00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 38.0 3.50e-01 74.8% 79.1%
1ej0A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 38.0 3.35e-01 76.5% 98.9%
6hhnA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 34.0 3.82e-01 72.3% 87.0%
3i3wA04 3.30.310.50 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Alpha-D-phosphohexomutase, C-terminal domain 0.52 31.0 3.66e-01 98.3% 89.6%
5w2fA01 3.30.780.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › SUI1-like domain 0.52 34.0 3.91e-01 99.2% 93.0%
3wx4A00 3.30.70.2770 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 36.0 3.88e-01 73.1% 87.8%
3fd3A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 36.0 3.78e-01 73.9% 98.1%
4kd5A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.50 36.0 3.60e-01 74.8% 96.7%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3280180 2501.1.1.0 ↗ a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II 0.84 59.0 6.90e-01 88.2% 100.0%
3741182 2501.1.1.1 ↗ a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › PTH2 0.79 72.0 6.74e-01 100.0% 81.4%
4946237 2501.1.1.1 ↗ a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › PTH2 0.78 70.0 7.16e-01 100.0% 98.3%
4947020 2501.1.1.1 ↗ a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › PTH2 0.78 70.0 7.19e-01 100.0% 99.1%
3599010 2501.1.1.0 ↗ a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II 0.75 70.0 6.80e-01 99.2% 100.0%
4937181 305.1.1.2 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L_2 0.64 34.0 4.02e-01 94.1% 76.2%
4931923 304.5.1.7 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.63 35.0 4.19e-01 100.0% 81.2%
4044550 304.5.1.7 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.63 35.0 4.23e-01 100.0% 82.5%
5038487 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.62 36.0 4.07e-01 100.0% 75.6%
4963170 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.62 36.0 4.07e-01 100.0% 75.6%
5012937 304.116.1.6 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in release factor › Ferredoxin-like domain in release factor › acVLRF1 0.61 43.0 4.81e-01 100.0% 91.6%
4413471 304.5.1.7 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.61 33.0 4.11e-01 100.0% 85.3%
5043656 304.116.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in release factor › Ferredoxin-like domain in release factor 0.60 43.0 4.76e-01 100.0% 92.6%
4021490 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.59 36.0 4.22e-01 100.0% 90.0%
3965385 304.14.1.1 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) › SPOR 0.59 34.0 4.22e-01 99.2% 95.7%
3567908 304.120.1.10 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › PF25904 0.58 34.0 4.16e-01 100.0% 95.7%
4972691 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.58 35.0 3.82e-01 100.0% 71.0%
4990439 304.116.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in release factor › Ferredoxin-like domain in release factor 0.58 41.0 4.50e-01 100.0% 87.0%
3840967 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.57 33.0 3.97e-01 97.5% 89.3%
3477897 304.44.1.0 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 0.57 37.0 4.14e-01 100.0% 85.6%
2101210 304.51.1.5 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › Cas_Csy4 0.57 38.0 4.25e-01 100.0% 89.9%
3732290 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.57 40.0 4.33e-01 72.3% 93.7%
3880966 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.56 33.0 4.02e-01 98.3% 92.0%
3740866 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.56 32.0 3.71e-01 97.5% 77.6%
4014118 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.56 33.0 4.00e-01 98.3% 92.0%
3521944 327.11.2.26 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_N4BP1_1st 0.55 32.0 3.87e-01 97.5% 92.9%
3283943 304.8.1.80 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DUF6196 0.55 31.0 3.84e-01 95.0% 92.9%
3820532 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.55 32.0 3.71e-01 98.3% 80.0%
3455834 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.55 35.0 3.88e-01 98.3% 82.2%
4995222 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.55 33.0 3.97e-01 100.0% 94.7%
3241590 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.55 33.0 3.77e-01 98.3% 82.4%
3374317 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.55 34.0 3.77e-01 98.3% 77.9%
3730662 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.54 38.0 4.09e-01 72.3% 89.0%
4095823 331.2.1.1 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain › PGM_PMM_IV 0.54 32.0 3.64e-01 98.3% 79.5%
3288688 304.43.1.1 ↗ a+b two layers › Alpha-beta plaits › Hypothetical protein TT1725 › Hypothetical protein TT1725 › DUF503 0.53 37.0 4.02e-01 72.3% 88.4%
4957351 304.18.1.0 ↗ a+b two layers › Alpha-beta plaits › Anticodon-binding domain of PheRS › Anticodon-binding domain of PheRS 0.53 35.0 4.08e-01 71.4% 100.0%
3433819 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.53 34.0 3.71e-01 99.2% 80.0%
4597971 331.2.1.0 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain 0.53 32.0 3.72e-01 99.2% 87.5%
3877940 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.53 30.0 3.71e-01 97.5% 94.3%
4838702 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.53 34.0 3.67e-01 81.5% 79.2%
3727503 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.53 31.0 3.46e-01 98.3% 72.6%
3543254 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.53 31.0 3.78e-01 98.3% 98.6%
3957166 304.43.1.0 ↗ a+b two layers › Alpha-beta plaits › Hypothetical protein TT1725 › Hypothetical protein TT1725 0.52 36.0 3.94e-01 100.0% 88.4%
3286817 304.4.1.9 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Chlor_dismutase 0.52 41.0 4.12e-01 85.7% 83.3%
3213699 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.52 33.0 3.60e-01 70.6% 80.0%
3511169 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.51 35.0 3.92e-01 98.3% 97.6%
4089718 331.2.1.1 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain › PGM_PMM_IV 0.51 32.0 3.72e-01 100.0% 93.7%
3672824 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.51 36.0 3.97e-01 100.0% 93.7%
4679172 331.2.1.1 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain › PGM_PMM_IV 0.50 31.0 3.67e-01 100.0% 91.3%