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MK016662.1__QBP05848.1__X__00053

Bact-Vir

MK016662.1__QBP05848.1__X__00053

Identity

Accession:
MK016662 ↗
Kingdom:
phage

Quality

73.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Autographivirales› Qadamvirus› Synechococcus_phage_S-B28

TaxID: 2545435

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 48-108
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2k49A00 2.30.29.80 Mainly Beta › Roll › PH-domain like › 0.71 54.0 4.33e-01 82.0% 88.1%
2dkhA03 3.40.30.20 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Phenol hydroxylase, C-terminal dimerisation domain 0.70 52.0 3.58e-01 80.3% 67.1%
2hc5A01 3.30.160.170 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › FlaG-like 0.70 59.0 5.09e-01 95.1% 60.2%
3cawA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.66 44.0 3.93e-01 70.5% 60.4%
5ic7A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.65 57.0 3.54e-01 98.4% 30.0%
3cynB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.62 46.0 3.35e-01 80.3% 78.0%
2w9jA00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.61 43.0 4.14e-01 75.4% 73.2%
7byjA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 43.0 3.75e-01 78.7% 48.4%
3brcA02 3.40.50.10150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › B12-dependent dehydatase associated subunit 0.60 45.0 3.76e-01 85.2% 87.5%
3tw8A01 3.30.450.200 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Longin module 0.60 41.0 3.24e-01 72.1% 34.1%
2l2mA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.60 41.0 3.97e-01 72.1% 64.3%
4ozuA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.60 51.0 3.20e-01 98.4% 32.0%
2v90C00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.58 44.0 3.87e-01 82.0% 73.1%
2kr0A01 2.30.29.70 Mainly Beta › Roll › PH-domain like › Proteasomal ubiquitin receptor Rpn13/ADRM1 0.58 49.0 4.05e-01 95.1% 81.4%
1u2kA02 1.10.420.10 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 2 › Peroxidase, domain 2 0.57 42.0 3.35e-01 86.9% 37.5%
3c4bA02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 43.0 4.25e-01 86.9% 91.0%
1q7fB00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.57 50.0 3.24e-01 100.0% 33.7%
4ns4A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 47.0 3.19e-01 100.0% 63.1%
8aimG01 3.10.450.20 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Bacteriophage PBS2, uracil-glycosylase inhibitor 0.56 39.0 3.66e-01 75.4% 69.1%
2g1lA00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.56 46.0 3.97e-01 96.7% 92.2%
3d9wA02 2.40.128.150 Mainly Beta › Beta Barrel › Lipocalin › Cysteine proteinases 0.55 46.0 3.99e-01 96.7% 90.2%
8adlB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 47.0 3.02e-01 98.4% 32.1%
2x5gA00 3.30.720.60 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.55 41.0 3.63e-01 96.7% 54.9%
1nqzA00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.54 37.0 2.72e-01 72.1% 25.1%
3lxrF00 1.10.4120.20 Mainly Alpha › Orthogonal Bundle › SopE-like GEF fold › 0.54 43.0 3.07e-01 86.9% 92.8%
2kgtA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.54 38.0 3.67e-01 75.4% 76.4%
3mvgA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.54 44.0 3.35e-01 96.7% 59.5%
2wtzA02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.53 39.0 2.80e-01 85.2% 22.6%
2qggA02 2.30.30.240 Mainly Beta › Roll › SH3 type barrels. › PRC-barrel domain 0.53 39.0 3.60e-01 82.0% 85.5%
2x5cA01 3.30.70.3590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 45.0 4.02e-01 100.0% 71.4%
3n7cA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 44.0 3.74e-01 98.4% 82.4%
4dxkA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 39.0 3.29e-01 88.5% 98.4%
5fl3A01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 38.0 3.34e-01 86.9% 50.0%
3i8tA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 42.0 3.41e-01 100.0% 85.0%
1xttB00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 35.0 2.43e-01 70.5% 84.6%
1e0bA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 36.0 3.69e-01 85.2% 77.0%
2ciuA00 3.10.450.320 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Mitochondrial import inner membrane translocase subunit Tim21 0.51 37.0 3.10e-01 83.6% 51.2%
1aqbA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.50 41.0 3.07e-01 96.7% 82.3%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
7726 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.77 53.0 5.45e-01 72.1% 87.9%
4341865 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.74 51.0 5.36e-01 72.1% 90.9%
3284714 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.74 54.0 5.34e-01 77.0% 81.0%
4188237 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.73 53.0 5.50e-01 77.0% 90.9%
4243634 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.72 51.0 4.78e-01 75.4% 96.0%
5075465 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.71 56.0 5.65e-01 86.9% 96.7%
3236050 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.71 55.0 4.55e-01 85.2% 84.5%
4106397 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.67 52.0 4.90e-01 86.9% 88.0%
3425722 386.1.1.117 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › DUF7028 0.66 49.0 4.42e-01 86.9% 57.6%
3408936 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.66 50.0 4.52e-01 85.2% 63.3%
4001239 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.65 47.0 4.11e-01 77.0% 52.6%
3801966 252.1.1.2 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › DUF7028 0.65 46.0 4.33e-01 86.9% 61.3%
3209694 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.65 55.0 4.77e-01 100.0% 70.0%
4497086 4100.1.1.5 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › HicB-like_2 0.64 48.0 4.39e-01 80.3% 96.2%
3432156 386.1.1.117 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › DUF7028 0.63 44.0 4.55e-01 86.9% 81.8%
3211234 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.63 49.0 3.74e-01 83.6% 70.3%
5018724 872.3.1.0 ↗ a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like 0.63 49.0 4.27e-01 85.2% 70.5%
3887124 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.63 46.0 3.35e-01 78.7% 28.6%
4868007 5.1.2.4 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › NHL 0.61 54.0 3.53e-01 98.4% 39.4%
3413965 5.1.4.463 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_NWD2_C 0.61 54.0 3.25e-01 100.0% 23.2%
3697385 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.61 54.0 3.25e-01 100.0% 79.3%
3739544 2004.1.1.433 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_23 0.60 53.0 3.04e-01 100.0% 95.7%
3499345 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.60 50.0 4.52e-01 96.7% 68.2%
3871823 2004.1.1.433 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_23 0.60 53.0 3.12e-01 100.0% 86.1%
4500042 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.60 53.0 3.15e-01 100.0% 84.5%
3918382 2004.1.1.433 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_23 0.60 52.0 3.02e-01 98.4% 96.1%
4004760 64.1.1.5 ↗ beta meanders › WW domain-like › WW domain › WW domain › DUF333 0.60 40.0 4.28e-01 83.6% 95.6%
5072132 331.10.2.0 ↗ a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.60 50.0 4.69e-01 100.0% 82.5%
3777742 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.59 52.0 3.19e-01 100.0% 90.8%
3930592 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.59 51.0 3.29e-01 100.0% 29.4%
3640612 2004.1.1.429 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_15 0.59 52.0 2.91e-01 100.0% 93.1%
3606500 375.8.1.1 ↗ few secondary structure elements › Rubredoxin-like › Zinc-binding domain of translation initiation factor 2 beta › Zinc-binding domain of translation initiation factor 2 beta › eIF-5_eIF-2B 0.59 40.0 4.09e-01 70.5% 85.0%
5072494 844.1.1.2 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › LOR 0.59 50.0 3.64e-01 96.7% 70.8%
3316055 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.59 49.0 3.36e-01 100.0% 32.5%
3561257 252.1.1.1 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.59 47.0 4.63e-01 95.1% 86.2%
3445225 2484.1.1.110 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MULE 0.59 46.0 3.11e-01 90.2% 100.0%
3846927 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.59 51.0 4.45e-01 100.0% 74.7%
3990293 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.58 40.0 4.13e-01 78.7% 78.2%
3720043 7.1.1.5 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ_2 0.58 44.0 3.73e-01 83.6% 94.3%
3548416 220.1.1.158 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_LRR1 0.58 49.0 4.00e-01 96.7% 79.2%
3907024 260.1.1.1 ↗ a+b duplicates or obligate multimers › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › Plectin 0.58 45.0 2.83e-01 83.6% 17.5%
3646319 6.1.1.25 ↗ beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › DUF569 0.58 47.0 3.50e-01 95.1% 84.6%
3541856 376.1.3.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD 0.57 46.0 3.67e-01 96.7% 77.2%
4929797 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.57 44.0 4.45e-01 83.6% 86.4%
3957726 222.1.1.12 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › PS-DH 0.57 38.0 2.82e-01 70.5% 62.8%
3922387 260.1.1.1 ↗ a+b duplicates or obligate multimers › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › Plectin 0.56 44.0 2.57e-01 85.2% 17.6%
5057301 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.56 49.0 3.27e-01 100.0% 36.5%
3722450 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.55 39.0 3.02e-01 75.4% 33.8%
3279065 206.1.1.11 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › APH 0.55 47.0 3.13e-01 100.0% 75.3%
3954692 9.4.1.0 ↗ beta barrels › Lipocalins/Streptavidin › D-aminopeptidase, middle and C-terminal domains › D-aminopeptidase, middle and C-terminal domains 0.55 45.0 3.87e-01 95.1% 84.8%
3934912 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 42.0 3.16e-01 82.0% 40.0%
3573585 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.54 35.0 3.64e-01 77.0% 74.1%
4020842 3209.1.1.0 ↗ a+b two layers › RPL28 › RPL28 › RPL28 0.53 44.0 3.46e-01 95.1% 57.9%
3667806 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.53 44.0 3.03e-01 95.1% 92.8%
3717566 5.1.3.28 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › BNR_3 0.53 39.0 2.65e-01 82.0% 46.8%
5000042 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.52 36.0 2.61e-01 93.4% 22.4%
4976853 220.5.1.1 ↗ beta barrels › PH domain-like › NucS N-terminal domain › NucS N-terminal domain › NucS_N 0.52 42.0 3.50e-01 95.1% 70.8%
3203084 3468.1.1.0 ↗ a+b two layers › HLTF protein HIRAN domain › HLTF protein HIRAN domain › HLTF protein HIRAN domain 0.52 44.0 3.28e-01 95.1% 88.7%
3218122 376.1.3.11 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › zf-HC5HC2H_2 0.51 37.0 2.96e-01 80.3% 73.6%
3564972 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.50 42.0 4.05e-01 100.0% 84.3%