Back to structures

NODE_12_length_310542_cov_175.846709.1__X__X__00089

Bact-Vir

NODE_12_length_310542_cov_175.846709.1__X__X__00089

Identity

Kingdom:
phage

Quality

90.4 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 66-154
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4b9wA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.74 45.0 5.47e-01 84.3% 96.4%
2eqkA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.74 49.0 5.33e-01 88.8% 82.2%
2diqA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.73 47.0 4.54e-01 88.8% 58.0%
2rceA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.68 44.0 4.15e-01 85.4% 54.7%
3otpA01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.67 46.0 3.55e-01 86.5% 31.5%
4qqgG00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.66 47.0 5.12e-01 87.6% 91.7%
2lccA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.65 46.0 4.99e-01 89.9% 86.8%
7oc3A01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.64 46.0 4.61e-01 87.6% 72.8%
3m9qA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.63 46.0 5.00e-01 87.6% 95.8%
3ic8A01 3.40.30.110 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.63 44.0 3.52e-01 89.9% 36.7%
2as9B01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.62 39.0 3.77e-01 85.4% 55.4%
5hmaA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.62 43.0 4.11e-01 85.4% 61.5%
4lduA03 2.30.30.1040 Mainly Beta › Roll › SH3 type barrels. › 0.62 45.0 4.95e-01 82.0% 100.0%
2gk6A02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.61 41.0 4.24e-01 84.3% 73.5%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.60 45.0 4.02e-01 80.9% 99.2%
3k6yA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.60 44.0 4.16e-01 85.4% 64.5%
1ylnA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 43.0 3.99e-01 87.6% 59.6%
4ic5A02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.58 41.0 3.97e-01 86.5% 63.5%
1lvoA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.58 34.0 3.44e-01 86.5% 58.0%
5ejlA02 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.57 39.0 3.53e-01 71.9% 54.0%
1vw4M01 2.30.30.790 Mainly Beta › Roll › SH3 type barrels. › 0.56 47.0 4.14e-01 92.1% 78.8%
2l1tA00 2.30.110.70 Mainly Beta › Roll › Pnp Oxidase; Chain A › 0.56 42.0 3.99e-01 93.3% 66.1%
4cshA00 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.55 39.0 3.25e-01 88.8% 40.9%
5yjlD01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 36.0 3.08e-01 87.6% 42.3%
1wqsA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 42.0 4.08e-01 88.8% 73.8%
4xsgB00 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.52 37.0 2.89e-01 74.2% 50.2%
1mi8A00 2.170.16.10 Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain 0.52 40.0 3.49e-01 83.1% 93.6%
3bbaA00 3.90.70.50 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Streptopain (SpeB) 0.52 44.0 3.21e-01 93.3% 96.7%
4rt0A00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.51 36.0 3.38e-01 95.5% 58.7%
3aupD01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.51 40.0 3.20e-01 86.5% 68.1%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.50 35.0 2.64e-01 73.0% 77.4%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4995699 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.90 66.0 7.51e-01 92.1% 95.7%
3581143 4.1.1.43 beta barrels › SH3 › SH3 › SH3 › SMN_Tudor 0.75 45.0 5.18e-01 85.4% 83.1%
3234107 4.1.1.169 beta barrels › SH3 › SH3 › SH3 › DUF4819 0.73 49.0 5.43e-01 87.6% 87.1%
4949773 4.11.1.0 beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase 0.70 48.0 4.09e-01 88.8% 43.4%
3713334 4.8.1.0 beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.69 45.0 5.36e-01 83.1% 100.0%
3933763 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.68 46.0 4.96e-01 96.6% 82.7%
3373583 4.1.1.42 beta barrels › SH3 › SH3 › SH3 › Agenet 0.67 48.0 5.35e-01 88.8% 97.1%
4982354 4.7.1.0 beta barrels › SH3 › RNase P subunit p29 › RNase P subunit p29 0.66 45.0 5.09e-01 85.4% 96.9%
3558774 4.1.1.104 beta barrels › SH3 › SH3 › SH3 › KN17_SH3 0.66 42.0 4.92e-01 86.5% 96.7%
3826751 4.1.1.42 beta barrels › SH3 › SH3 › SH3 › Agenet 0.66 49.0 5.17e-01 89.9% 87.5%
3457163 4.1.1.42 beta barrels › SH3 › SH3 › SH3 › Agenet 0.66 45.0 4.74e-01 88.8% 78.8%
5080798 4.17.1.0 beta barrels › SH3 › GatD N-terminal domain-like › GatD N-terminal domain-like 0.64 48.0 5.12e-01 85.4% 93.3%
3518287 4.1.1.347 beta barrels › SH3 › SH3 › SH3 › KOW7_SPT5, KOW6_SPT5 0.64 46.0 4.18e-01 86.5% 57.4%
3357709 4.1.1.42 beta barrels › SH3 › SH3 › SH3 › Agenet 0.64 51.0 5.21e-01 88.8% 88.2%
3806777 4.1.1.42 beta barrels › SH3 › SH3 › SH3 › Agenet 0.64 49.0 5.29e-01 89.9% 97.3%
3598734 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.62 40.0 2.92e-01 86.5% 24.3%
3650296 4.1.1.94 beta barrels › SH3 › SH3 › SH3 › SAWADEE 0.62 51.0 5.01e-01 89.9% 82.1%
3675120 4.1.1.42 beta barrels › SH3 › SH3 › SH3 › Agenet 0.61 49.0 5.06e-01 91.0% 90.6%
3960279 1.1.5.33 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.60 45.0 3.82e-01 86.5% 48.3%
3609031 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.60 40.0 3.88e-01 87.6% 60.0%
3449628 1.1.5.33 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.60 40.0 3.72e-01 86.5% 53.0%
3830352 4.1.1.94 beta barrels › SH3 › SH3 › SH3 › SAWADEE 0.60 50.0 5.10e-01 89.9% 92.9%
3322460 4.1.1.94 beta barrels › SH3 › SH3 › SH3 › SAWADEE 0.60 49.0 4.51e-01 89.9% 68.7%
4930890 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.59 40.0 4.34e-01 89.9% 82.7%
3447798 4.25.1.0 beta barrels › SH3 › Auxin response factor dimerization domain and ancillary domain › Auxin response factor dimerization domain and ancillary domain 0.59 44.0 4.89e-01 87.6% 100.0%
3358748 4.1.1.94 beta barrels › SH3 › SH3 › SH3 › SAWADEE 0.59 46.0 4.83e-01 85.4% 91.3%
4015954 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.59 44.0 3.27e-01 85.4% 30.2%
3439936 1.1.17.3 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.58 43.0 3.05e-01 85.4% 24.6%
3280955 1.1.5.33 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.58 45.0 3.32e-01 86.5% 32.4%
4387111 4.1.1.97 beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.58 46.0 4.83e-01 87.6% 96.2%
3210702 1.1.17.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.57 47.0 3.41e-01 93.3% 44.3%
4625374 1.1.5.33 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.57 42.0 3.15e-01 86.5% 30.4%
3519122 4.31.1.1 beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.57 48.0 4.86e-01 94.4% 92.2%
138887 1.1.5.32 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZNR 0.57 42.0 3.83e-01 87.6% 58.1%
3950281 1.1.5.33 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.57 44.0 3.28e-01 86.5% 32.4%
3243256 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.57 48.0 3.78e-01 89.9% 74.9%
3363751 4.1.1.246 beta barrels › SH3 › SH3 › SH3 › Tudor_Coilin 0.57 46.0 4.37e-01 87.6% 88.6%
3183093 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.56 46.0 3.99e-01 88.8% 57.1%
3469033 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.56 43.0 3.08e-01 86.5% 28.4%
3198319 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.56 46.0 3.20e-01 94.4% 36.4%
3599465 4.18.1.0 beta barrels › SH3 › Plus3 › Plus3 0.54 45.0 3.92e-01 93.3% 60.0%
3821287 4.1.1.17 beta barrels › SH3 › SH3 › SH3 › Ribosomal_L19 0.54 46.0 4.04e-01 97.8% 68.6%
3635435 4.18.1.1 beta barrels › SH3 › Plus3 › Plus3 › Plus-3 0.53 44.0 3.77e-01 91.0% 73.1%
4028467 1.1.5.33 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.53 43.0 3.05e-01 87.6% 71.6%
3707125 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.53 42.0 3.60e-01 87.6% 70.0%
3947895 4.26.1.4 beta barrels › SH3 › Chromatin protein Cren7 › Chromatin protein Cren7 › zf-IS66 0.53 36.0 3.84e-01 87.6% 88.6%
3704929 4.18.1.1 beta barrels › SH3 › Plus3 › Plus3 › Plus-3 0.53 44.0 3.77e-01 93.3% 55.3%
3986836 375.1.1.253 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-IS66 0.52 32.0 3.62e-01 84.3% 96.4%
3098472 375.1.1.3 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L33 0.50 30.0 3.51e-01 83.1% 92.9%
4217523 1.1.5.25 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.50 35.0 3.22e-01 91.0% 52.8%
D2 medium residues 1-60
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4pkfB00 4.10.490.20 Few Secondary Structures › Irregular › High-Potential Iron-Sulfur Protein; Chain A › 0.70 55.0 5.24e-01 85.0% 75.4%
1isuA00 4.10.490.10 Few Secondary Structures › Irregular › High-Potential Iron-Sulfur Protein; Chain A › High potential iron-sulphur protein 0.66 46.0 4.59e-01 85.0% 71.0%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.59 41.0 4.22e-01 80.0% 77.2%
3ialA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.59 43.0 3.52e-01 80.0% 71.4%
2m2lA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 38.0 3.74e-01 73.3% 71.6%
2hdlA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.55 40.0 3.75e-01 81.7% 79.2%
4z3xA03 1.10.569.10 Mainly Alpha › Orthogonal Bundle › Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2 › Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2 0.54 40.0 2.91e-01 81.7% 44.6%
3fdbA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.54 39.0 2.97e-01 78.3% 56.1%
2k3aA01 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.53 40.0 3.47e-01 85.0% 64.0%
1e0bA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 37.0 3.71e-01 75.0% 75.4%
6i7eA01 1.20.58.530 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 36.0 2.62e-01 75.0% 65.7%
4o62A00 3.30.40.100 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › 0.51 29.0 3.01e-01 80.0% 57.1%
3zuaA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.50 39.0 3.16e-01 88.3% 48.9%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3874110 2004.1.1.534 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › PF30386 0.59 43.0 2.95e-01 78.3% 60.4%
4397221 325.1.7.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.59 40.0 3.89e-01 71.7% 64.6%
4031789 4959.1.1.0 a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit 0.56 35.0 3.57e-01 71.7% 63.3%
3471771 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.55 39.0 4.10e-01 76.7% 100.0%
3591064 325.1.7.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.54 34.0 3.39e-01 71.7% 60.0%
3520811 4.8.1.2 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.53 37.0 3.58e-01 75.0% 65.7%
3400005 4.8.1.2 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.52 36.0 3.69e-01 75.0% 78.3%
3461718 5.1.3.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.52 37.0 2.52e-01 76.7% 22.6%
4239781 3006.1.1.6 a+b two layers › Sm-Like archaeal protein Smap3, C-terminal domain › Sm-Like archaeal protein Smap3, C-terminal domain › Sm-Like archaeal protein Smap3, C-terminal domain › CPSF73-100_C 0.51 38.0 3.69e-01 83.3% 88.6%
3310899 4.8.1.1 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo 0.51 35.0 3.23e-01 75.0% 58.8%
3471995 4.8.1.1 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo 0.51 37.0 3.29e-01 81.7% 60.0%
3741268 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.51 34.0 2.51e-01 71.7% 41.1%