←Back to structures

MK448884.1__QBX25274.1__Javan246_0031__00028

Bact-Vir

MK448884.1__QBX25274.1__Javan246_0031__00028

Identity

Accession:
MK448884 ↗
Kingdom:
phage

Quality

85.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Streptococcus_phage_Javan246

TaxID: 2548068

Cluster

View cluster (36 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 9-66
PDB
Domain cluster: rep: OQ504960.1__WID41994.1__X__00022__D3-68
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1qr4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.77 54.0 4.65e-01 100.0% 48.3%
5eh1A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.71 48.0 4.10e-01 100.0% 43.2%
1u1sA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.69 53.0 5.08e-01 100.0% 72.7%
6b9tF01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.68 42.0 3.27e-01 100.0% 28.8%
3bcwA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.68 43.0 3.51e-01 100.0% 35.6%
1kq1H00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.68 52.0 4.98e-01 98.3% 72.7%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.67 50.0 4.20e-01 100.0% 48.0%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.66 47.0 4.26e-01 100.0% 55.0%
2hlcA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.65 45.0 3.78e-01 100.0% 41.3%
3rj2X00 2.60.120.1150 Mainly Beta › Sandwich › Jelly Rolls › 0.64 46.0 3.51e-01 100.0% 33.1%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.64 54.0 4.54e-01 100.0% 56.2%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.63 50.0 4.13e-01 100.0% 46.8%
3in6A02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.63 52.0 4.11e-01 100.0% 45.3%
2mv2A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.63 45.0 3.40e-01 100.0% 30.4%
2z8lA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.62 45.0 3.59e-01 100.0% 38.5%
2f4nB02 2.40.30.90 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Bacterial fluorinating enzyme like 0.62 56.0 4.70e-01 98.3% 69.1%
1rfeA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.62 49.0 3.77e-01 100.0% 37.5%
1a21A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 44.0 3.75e-01 100.0% 45.9%
1ca1A02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.61 51.0 4.03e-01 100.0% 45.0%
2f1eA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.61 50.0 3.99e-01 100.0% 45.7%
4kncA02 2.60.120.1380 Mainly Beta › Sandwich › Jelly Rolls › C-terminal carbohydrate-binding module 0.60 50.0 3.98e-01 100.0% 45.3%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.60 49.0 4.22e-01 100.0% 56.5%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.60 54.0 4.35e-01 100.0% 54.1%
2fg9A01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 47.0 3.51e-01 100.0% 32.1%
5hdwA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.60 50.0 3.80e-01 100.0% 40.5%
6z9cA01 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.59 50.0 3.92e-01 100.0% 44.3%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.59 52.0 4.12e-01 100.0% 52.1%
2fb7A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.59 50.0 4.61e-01 100.0% 91.3%
2dlgA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 42.0 3.87e-01 100.0% 57.5%
5ja1B00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.58 35.0 3.41e-01 100.0% 51.5%
1ty0B01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.57 47.0 3.57e-01 100.0% 39.4%
1wp5A00 2.120.10.90 Mainly Beta › 6 Propeller › Neuraminidase › DNA gyrase/topoisomerase IV, subunit A, C-terminal 0.57 46.0 2.89e-01 100.0% 16.1%
2iruA02 3.30.70.3300 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 47.0 3.68e-01 100.0% 71.7%
3b8fB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.56 46.0 3.44e-01 100.0% 36.6%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.56 46.0 3.44e-01 100.0% 47.3%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.55 47.0 3.61e-01 100.0% 40.9%
1ywlA00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.55 44.0 3.81e-01 100.0% 54.2%
3bn6A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 48.0 3.53e-01 100.0% 55.7%
3zq5A03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.55 37.0 2.81e-01 87.9% 26.8%
2pstX00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.55 33.0 3.32e-01 100.0% 55.7%
6rptC00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 40.0 3.34e-01 100.0% 43.8%
3foeA02 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.54 37.0 3.57e-01 72.4% 72.5%
3weeA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 41.0 2.90e-01 84.5% 99.5%
4jzjC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 42.0 3.50e-01 100.0% 49.0%
4uzgA01 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 45.0 3.37e-01 100.0% 41.0%
2bkfA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 45.0 4.06e-01 100.0% 88.0%
2piaA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.52 44.0 3.72e-01 100.0% 59.6%
3bh1A03 3.40.140.40 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Domain of unknown function (DUF1846), C-terminal subdomain 0.52 44.0 3.36e-01 100.0% 73.3%
2pnqA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.51 43.0 2.69e-01 100.0% 32.5%
4pjeE01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 44.0 3.63e-01 100.0% 55.6%
3wqbA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 44.0 3.24e-01 100.0% 71.7%
1mg7A01 3.30.70.1000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Switch protein XOL-1, GHMP-like 0.50 41.0 3.07e-01 100.0% 76.6%
ECOD (54)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3972526 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.82 74.0 6.92e-01 100.0% 91.4%
3725727 3792.1.1.0 ↗ beta sandwiches › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain 0.81 48.0 4.22e-01 100.0% 41.2%
3637393 3792.1.1.2 ↗ beta sandwiches › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain › APC1_3rd 0.79 47.0 4.02e-01 100.0% 38.9%
4632256 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.78 69.0 6.36e-01 100.0% 96.0%
4147528 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.76 66.0 6.30e-01 100.0% 100.0%
3603549 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 66.0 5.87e-01 100.0% 74.4%
3265105 11.1.1.802 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF8390 0.68 48.0 4.14e-01 100.0% 46.3%
3552986 11.1.1.275 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › IL3Ra_N 0.67 46.0 4.08e-01 100.0% 49.4%
4215906 3578.1.1.1 ↗ beta sandwiches › Third domain in metalloprotease StcE › Third domain in metalloprotease StcE › Third domain in metalloprotease StcE › TagA 0.65 50.0 4.11e-01 100.0% 45.7%
3607227 4012.3.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.65 50.0 5.29e-01 96.6% 98.0%
3272931 224.1.1.2 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.63 39.0 3.31e-01 100.0% 34.3%
3969006 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.63 43.0 4.72e-01 100.0% 93.3%
4939155 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.63 54.0 4.26e-01 100.0% 46.2%
4332271 10.10.1.1 ↗ beta sandwiches › jelly-roll › Lipase/lipooxygenase domain (PLAT/LH2 domain) › Lipase/lipooxygenase domain (PLAT/LH2 domain) › PLAT 0.63 53.0 4.14e-01 100.0% 43.9%
4158495 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.63 48.0 4.24e-01 100.0% 55.6%
4007508 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.63 43.0 4.54e-01 100.0% 84.0%
5046850 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.63 49.0 4.34e-01 100.0% 57.8%
5007278 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.62 49.0 3.71e-01 100.0% 37.7%
420847 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.62 42.0 3.46e-01 100.0% 35.8%
4004704 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.61 42.0 4.58e-01 100.0% 93.3%
3968122 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.61 42.0 4.54e-01 100.0% 93.3%
4463006 3115.2.1.0 ↗ a+b two layers › GP2-like › GP2 › GP2 0.61 42.0 4.64e-01 98.3% 95.6%
3285401 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.60 45.0 4.21e-01 100.0% 65.3%
3352566 2487.1.1.7 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › PA 0.59 52.0 3.58e-01 100.0% 95.6%
5012895 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.59 48.0 4.92e-01 100.0% 96.4%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.57 42.0 4.39e-01 100.0% 94.0%
3959955 304.163.1.3 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain › PF31118 0.57 39.0 4.25e-01 100.0% 95.6%
3475431 133.1.1.0 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) 0.56 49.0 3.28e-01 100.0% 41.2%
3223606 210.2.1.1 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.56 38.0 2.46e-01 70.7% 40.7%
3594014 2007.2.3.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II 0.55 42.0 2.89e-01 100.0% 21.3%
3528111 10.21.1.0 ↗ beta sandwiches › jelly-roll › Jelly-roll domain in ADAMTS13 › Jelly-roll domain in ADAMTS13 0.55 48.0 3.70e-01 100.0% 44.8%
3505268 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.55 44.0 3.59e-01 100.0% 66.7%
3325330 3346.1.1.5 ↗ a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › ODR4-like 0.55 40.0 2.90e-01 96.6% 24.6%
3409292 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 41.0 3.48e-01 100.0% 48.0%
3174696 2487.1.1.0 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" 0.55 47.0 3.33e-01 100.0% 97.9%
3604593 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.54 44.0 4.50e-01 100.0% 96.4%
3264437 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 41.0 3.43e-01 100.0% 45.7%
3597533 4357.1.1.0 ↗ beta barrels › WWE domain › WWE domain › WWE domain 0.54 44.0 3.74e-01 96.6% 90.5%
5053654 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 36.0 3.01e-01 74.1% 96.7%
5041794 206.1.3.40 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATPgrasp_YheCD 0.53 45.0 2.92e-01 100.0% 63.4%
3215161 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 44.0 3.92e-01 100.0% 65.5%
3215294 10.12.1.97 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › CNBH_CNNM2_C 0.53 40.0 3.01e-01 86.2% 82.4%
3510040 3115.3.1.2 ↗ a+b two layers › GP2-like › P56 › P56 › DUF2922 0.53 43.0 4.03e-01 100.0% 73.8%
3998052 304.112.1.0 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.52 45.0 3.68e-01 100.0% 89.6%
3320228 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.52 37.0 2.14e-01 77.6% 12.4%
3294481 210.2.1.1 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.52 38.0 2.49e-01 86.2% 33.1%
4394562 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.52 39.0 2.37e-01 86.2% 40.9%
3250477 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 39.0 3.18e-01 86.2% 84.9%
3519916 11.2.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.51 38.0 3.36e-01 100.0% 52.6%
3291463 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.51 35.0 2.44e-01 72.4% 83.7%
5047600 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 40.0 3.10e-01 87.9% 46.7%
4996589 3662.1.1.4 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC_bac 0.50 38.0 3.11e-01 86.2% 47.5%
3888324 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 43.0 3.61e-01 100.0% 54.3%
3937995 223.1.1.138 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › VWA_N, VGCC_alpha2 0.50 36.0 2.09e-01 81.0% 13.6%