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MH929319.1__AYP28363.1__3M_107__00105

Bact-Vir

MH929319.1__AYP28363.1__3M_107__00105

Identity

Accession:
MH929319 ↗
Kingdom:
phage

Quality

70.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Ackermannviridae› Miltonvirus› Serratia_phage_vB_SmaA_3M

TaxID: 2419930

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 3-50
PDB
D2 high residues 68-107
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4s3nA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.72 52.0 3.59e-01 80.0% 21.8%
2r41A00 3.10.450.150 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › enterococcus faecalis protein 0.70 49.0 3.67e-01 80.0% 29.1%
1s3lA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.70 50.0 3.31e-01 77.5% 99.4%
1x0tA02 6.20.50.20 Special › Other non-globular › N-terminal domain of TfIIb › 0.69 47.0 4.60e-01 80.0% 64.4%
3kksB00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.68 58.0 3.95e-01 100.0% 30.3%
3rh9A01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.68 48.0 2.94e-01 80.0% 78.2%
7ue1B01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.67 57.0 3.93e-01 100.0% 31.9%
1zy9A03 2.60.40.2760 Mainly Beta › Sandwich › Immunoglobulin-like › 0.66 47.0 4.63e-01 77.5% 69.8%
4f80A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 55.0 4.27e-01 100.0% 74.2%
5cqfA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.65 46.0 2.68e-01 80.0% 7.6%
1krlA00 6.20.50.130 Special › Other non-globular › N-terminal domain of TfIIb › 0.65 46.0 4.55e-01 77.5% 75.0%
1y96D00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.65 46.0 3.73e-01 77.5% 38.6%
3dsmA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.64 53.0 3.15e-01 97.5% 21.7%
2xf4A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.63 53.0 3.40e-01 100.0% 59.5%
1df0A02 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.63 47.0 3.75e-01 97.5% 38.0%
3lxqA01 3.30.1120.80 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.63 46.0 3.49e-01 85.0% 32.3%
2xlpB01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.62 44.0 2.63e-01 80.0% 9.6%
2rajA02 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.62 49.0 3.66e-01 100.0% 93.7%
1tk7A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.61 46.0 4.74e-01 97.5% 91.9%
2lt1A00 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.61 47.0 4.07e-01 97.5% 65.3%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.60 45.0 4.25e-01 100.0% 64.9%
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.60 43.0 3.85e-01 90.0% 49.2%
3ecrB03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.60 45.0 3.67e-01 100.0% 67.6%
3kxtA00 2.30.30.610 Mainly Beta › Roll › SH3 type barrels. › Chromatin protein Cren7 0.59 42.0 3.90e-01 80.0% 66.1%
4cy8A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.59 41.0 2.63e-01 80.0% 12.3%
3fetA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.59 41.0 2.82e-01 80.0% 18.8%
6vp6A03 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.58 45.0 2.72e-01 92.5% 11.3%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.58 44.0 3.95e-01 100.0% 73.0%
4tm3A00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.58 41.0 2.40e-01 80.0% 8.0%
3voqA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 45.0 3.48e-01 100.0% 37.1%
2c9oB02 2.40.50.360 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RuvBL1 DNA/RNA binding domain 0.57 48.0 3.56e-01 100.0% 76.1%
1o97D01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.57 40.0 2.71e-01 80.0% 16.4%
2w5aA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.57 42.0 3.88e-01 95.0% 85.9%
1mpgA01 3.30.310.20 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › DNA-3-methyladenine glycosylase AlkA, N-terminal domain 0.57 39.0 3.05e-01 80.0% 32.1%
3nybA02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.57 39.0 3.09e-01 85.0% 30.0%
1lgpA00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.56 39.0 2.98e-01 77.5% 38.1%
1x9mA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.55 43.0 2.82e-01 100.0% 20.8%
2f4mA02 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.55 38.0 3.72e-01 80.0% 78.0%
5l37C00 2.40.50.220 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › EutN/Ccml 0.55 43.0 3.60e-01 97.5% 86.0%
2psbA00 3.50.90.10 Alpha Beta › 3-Layer(bba) Sandwich › YerB-like fold › YerB-like 0.55 42.0 2.60e-01 92.5% 15.2%
1khiA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.54 43.0 3.68e-01 97.5% 65.3%
3payB02 2.60.40.2090 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 44.0 3.22e-01 100.0% 72.7%
2nmlA00 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.54 43.0 3.39e-01 97.5% 91.0%
2im9A02 2.30.260.10 Mainly Beta › Roll › putative xylanase like fold › putative xylanase like domain 0.53 41.0 2.99e-01 100.0% 26.5%
2eczA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.53 36.0 3.21e-01 90.0% 44.3%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3169198 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.71 50.0 5.13e-01 77.5% 91.4%
3510695 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.70 58.0 4.79e-01 100.0% 56.2%
3587060 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.69 52.0 4.33e-01 85.0% 57.3%
3935131 2484.1.1.9 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.69 58.0 3.87e-01 100.0% 27.9%
3710675 375.1.1.7 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › TFIIS_C 0.69 49.0 4.65e-01 80.0% 64.6%
4256808 12.1.1.52 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › GLGE_C 0.68 49.0 4.82e-01 77.5% 72.7%
4932673 375.1.1.26 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rpr2 0.68 47.0 3.69e-01 80.0% 33.3%
3926267 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.68 58.0 3.91e-01 100.0% 28.7%
4481026 4.1.1.407 ↗ beta barrels › SH3 › SH3 › SH3 › PF29661 0.68 50.0 4.48e-01 90.0% 55.0%
2575628 2484.1.1.9 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.67 57.0 3.90e-01 100.0% 30.1%
3597599 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.67 55.0 4.27e-01 100.0% 41.0%
3801752 375.1.1.269 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › PF29332 0.65 52.0 4.93e-01 92.5% 100.0%
5049449 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 45.0 4.31e-01 77.5% 66.0%
4117020 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.64 44.0 3.99e-01 100.0% 50.0%
3639553 206.1.1.11 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › APH 0.64 52.0 3.34e-01 95.0% 41.4%
3924385 1.1.15.0 ↗ beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like 0.64 52.0 3.16e-01 100.0% 20.3%
3673032 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 55.0 4.64e-01 100.0% 57.1%
3927135 247.1.1.1 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B 0.63 50.0 3.07e-01 100.0% 24.7%
4966836 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.63 52.0 4.79e-01 100.0% 72.7%
3544618 4292.2.1.0 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.63 52.0 4.24e-01 100.0% 71.8%
3356481 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 45.0 3.73e-01 100.0% 39.8%
5051613 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.63 52.0 3.79e-01 100.0% 33.1%
4609498 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.63 51.0 4.25e-01 100.0% 71.2%
3189282 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.63 43.0 4.44e-01 75.0% 100.0%
4126006 325.1.7.14 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › RPOC_hybrid 0.63 53.0 4.54e-01 97.5% 70.8%
3938255 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.62 51.0 3.18e-01 97.5% 16.2%
3451173 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.62 46.0 3.76e-01 90.0% 42.2%
4338934 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.62 52.0 4.52e-01 100.0% 76.9%
5061930 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 43.0 3.38e-01 80.0% 32.6%
3546143 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 48.0 2.80e-01 90.0% 43.7%
None — 0.61 47.0 2.96e-01 92.5% 29.1%
5030311 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.61 43.0 3.95e-01 77.5% 56.4%
1112010 4.1.1.32 ↗ beta barrels › SH3 › SH3 › SH3 › CarD_TRCF_RID 0.61 47.0 4.07e-01 97.5% 65.3%
4138663 4099.1.1.3 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Spc24 0.61 48.0 4.28e-01 97.5% 76.9%
3591633 1021.1.1.0 ↗ a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases 0.60 49.0 3.71e-01 100.0% 90.0%
3998167 247.1.1.0 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase 0.60 46.0 2.96e-01 100.0% 29.2%
3889630 868.1.1.0 ↗ a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related 0.59 42.0 2.84e-01 80.0% 18.8%
3642524 108.1.1.96 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_1, EF-hand_6, EF-hand_7 0.59 42.0 3.15e-01 80.0% 25.6%
4306285 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 44.0 3.83e-01 100.0% 50.0%
4938828 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 42.0 3.91e-01 90.0% 56.7%
4009232 2005.1.1.10 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ETF 0.59 41.0 2.77e-01 77.5% 16.8%
3733718 4292.2.1.0 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.58 46.0 3.83e-01 97.5% 49.4%
4519674 4.1.1.186 ↗ beta barrels › SH3 › SH3 › SH3 › DUF5397 0.58 45.0 4.25e-01 100.0% 69.0%
3620947 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.58 45.0 4.26e-01 97.5% 74.5%
3598807 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.58 46.0 4.08e-01 100.0% 81.2%
5052753 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.58 41.0 2.85e-01 80.0% 21.9%
4851967 4.1.1.32 ↗ beta barrels › SH3 › SH3 › SH3 › CarD_TRCF_RID 0.57 44.0 4.10e-01 100.0% 69.4%
3201592 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.57 41.0 2.64e-01 80.0% 14.5%
4933707 2005.1.1.10 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ETF 0.56 39.0 2.66e-01 77.5% 16.8%
3656396 219.1.1.16 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C48 0.56 45.0 3.13e-01 100.0% 37.6%
4983452 2005.1.1.10 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ETF 0.55 43.0 2.86e-01 97.5% 19.5%
3260369 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.55 39.0 3.85e-01 90.0% 75.6%
3220598 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.55 38.0 2.71e-01 87.5% 20.6%
3281618 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.55 39.0 3.23e-01 90.0% 35.0%
5079728 208.1.1.1 ↗ beta duplicates or obligate multimers › Single-stranded left-handed beta-helix › Trimeric LpxA-like enzymes › Trimeric LpxA-like enzymes › Hexapep 0.54 36.0 2.47e-01 80.0% 15.4%
3576957 221.13.1.0 ↗ a+b two layers › beta-Grasp › Mitochondrial calcium uniporter N-terminal domain › Mitochondrial calcium uniporter N-terminal domain 0.54 41.0 3.03e-01 97.5% 32.1%
3600598 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.52 38.0 2.90e-01 97.5% 30.7%
3927286 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.52 36.0 3.16e-01 80.0% 49.3%
3641506 3957.1.1.0 ↗ a+b two layers › EKC/KEOPS complex subunit GON7 › EKC/KEOPS complex subunit GON7 › EKC/KEOPS complex subunit GON7 0.51 40.0 3.28e-01 92.5% 69.4%
4969039 2005.1.1.10 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ETF 0.51 36.0 2.48e-01 82.5% 16.8%
3643893 66.1.1.1 ↗ beta sandwiches › ISP domain › ISP domain › ISP domain › Rieske 0.51 41.0 3.43e-01 100.0% 67.5%
4026378 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 39.0 2.54e-01 100.0% 23.1%
3650304 66.1.1.0 ↗ beta sandwiches › ISP domain › ISP domain › ISP domain 0.51 38.0 3.44e-01 87.5% 63.3%