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NC_004740.1__NP_835577.1__SA1757B__00061

Bact-Vir

NC_004740.1__NP_835577.1__SA1757B__00061

Identity

Accession:
NC_004740 ↗
Kingdom:
phage

Quality

75.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Staphylococcus_phage_phiN315

TaxID: 225979

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 medium residues 1-62
PDB
Domain cluster: rep: MK448998.1__QBX31359.1__Javan636_0004__00059__D112-179
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08460.17 best SH3_5 36.1 7.90e-09 77.4% 61.8%
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2mk5A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.91 84.0 6.44e-01 100.0% 50.4%
1r77A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.90 84.0 7.00e-01 100.0% 64.6%
2dk7A00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.70 43.0 4.13e-01 75.8% 53.4%
3c96A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.64 46.0 3.35e-01 75.8% 70.2%
1reoA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.63 44.0 3.38e-01 74.2% 81.8%
3j7aF03 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.62 40.0 3.90e-01 100.0% 59.2%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.61 38.0 3.90e-01 80.6% 66.1%
2xg5A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 45.0 4.01e-01 82.3% 95.7%
1vwxg01 6.20.370.70 Special › Other non-globular › Rhinovirus 14, subunit 4 › 0.60 34.0 4.07e-01 95.2% 91.9%
1n02A00 2.30.60.10 Mainly Beta › Roll › HIV-inactivating Protein, Cyanovirin-n › Cyanovirin-N 0.59 41.0 3.59e-01 74.2% 99.0%
6cnhA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.58 39.0 3.66e-01 72.6% 55.0%
1gutA00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.58 37.0 3.62e-01 79.0% 58.2%
2qggA02 2.30.30.240 Mainly Beta › Roll › SH3 type barrels. › PRC-barrel domain 0.58 41.0 3.78e-01 77.4% 56.6%
3nixB00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.58 41.0 2.54e-01 75.8% 72.5%
1rl1A00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 41.0 3.73e-01 82.3% 96.7%
1tg0A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.56 40.0 3.98e-01 100.0% 72.7%
1a15A00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 39.0 3.82e-01 95.2% 68.7%
5jk0B01 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.56 41.0 3.00e-01 79.0% 61.3%
1h6lA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.55 47.0 2.94e-01 95.2% 26.9%
1zswA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.55 44.0 3.24e-01 88.7% 77.5%
2bw8A00 2.60.120.180 Mainly Beta › Sandwich › Jelly Rolls › Glycoside hydrolase family 11/12, catalytic domain 0.55 45.0 3.09e-01 91.9% 37.6%
2xcmC00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 40.0 3.60e-01 80.6% 95.7%
6aonA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 39.0 3.19e-01 79.0% 55.3%
1b9mA03 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.54 43.0 4.20e-01 98.4% 80.3%
2p4bB02 3.30.200.100 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › MucB/RseB, C-terminal domain 0.53 38.0 3.26e-01 74.2% 72.4%
3f4lA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.53 36.0 2.50e-01 71.0% 70.4%
1ci3M02 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.53 39.0 4.04e-01 79.0% 96.6%
4zpjA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 40.0 2.86e-01 82.3% 29.2%
1lomA00 2.30.60.10 Mainly Beta › Roll › HIV-inactivating Protein, Cyanovirin-n › Cyanovirin-N 0.53 36.0 3.20e-01 74.2% 60.4%
1vpkA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.52 37.0 3.05e-01 74.2% 60.5%
4harA00 3.10.50.50 Alpha Beta › Roll › Chitinase A; domain 3 › Rubella virus capsid protein 0.52 46.0 3.94e-01 98.4% 94.9%
2bwnB01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 35.0 2.67e-01 71.0% 83.0%
3rheA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 38.0 3.25e-01 82.3% 98.2%
2lojA01 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.51 30.0 3.47e-01 71.0% 87.2%
4huzA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.51 43.0 3.27e-01 98.4% 93.4%
1r8oB01 2.30.30.480 Mainly Beta › Roll › SH3 type barrels. › 0.51 34.0 3.41e-01 71.0% 98.5%
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.51 43.0 4.17e-01 98.4% 97.1%
4i8oA01 3.30.310.240 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Bacterial toxin RNase RnlA/LsoA, N-terminal domain 0.51 37.0 3.35e-01 79.0% 73.0%
2o07A01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.51 35.0 3.62e-01 77.4% 78.0%
1iy9A02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.51 34.0 3.62e-01 77.4% 84.6%
3ic9A03 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.50 36.0 2.96e-01 77.4% 55.7%
ECOD (68)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4032300 4.1.1.59 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_5 0.97 93.0 7.97e-01 100.0% 68.9%
3988893 4.1.1.59 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_5 0.92 76.0 7.03e-01 90.3% 72.0%
4041535 4.1.1.59 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_5 0.91 85.0 7.40e-01 100.0% 72.7%
3929809 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.77 43.0 5.30e-01 77.4% 87.5%
5043752 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.68 39.0 2.56e-01 72.6% 13.9%
4224041 4.6.1.2 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain › PRC 0.67 42.0 4.00e-01 77.4% 53.3%
3584335 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.67 38.0 4.57e-01 79.0% 97.1%
3790904 4.8.1.2 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.66 39.0 3.95e-01 71.0% 60.0%
2445318 206.1.1.9 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › RIO1 0.65 37.0 4.32e-01 74.2% 97.1%
3733247 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.64 46.0 3.02e-01 75.8% 65.5%
3507376 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.64 38.0 4.59e-01 77.4% 95.0%
3515805 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.64 39.0 4.64e-01 79.0% 97.5%
3509213 391.1.2.9 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related › Fn1_2 0.64 46.0 4.30e-01 95.2% 62.7%
3619861 391.1.1.7 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › Fn1_2 0.64 36.0 4.32e-01 74.2% 89.7%
3618450 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.63 45.0 3.97e-01 79.0% 91.0%
3585186 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.63 36.0 4.42e-01 72.6% 100.0%
3520872 391.1.1.7 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › Fn1_2 0.62 45.0 4.28e-01 96.8% 64.0%
3924377 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.62 40.0 4.25e-01 75.8% 72.7%
5034724 4.1.1.482 ↗ beta barrels › SH3 › SH3 › SH3 › DUF4314 0.61 41.0 4.29e-01 83.9% 78.2%
3638604 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.61 38.0 2.97e-01 79.0% 28.1%
3286756 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.61 46.0 3.89e-01 85.5% 98.2%
3517193 391.1.1.7 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › Fn1_2 0.61 50.0 4.29e-01 91.9% 89.0%
3288795 2003.1.3.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain 0.60 43.0 2.85e-01 77.4% 86.0%
3964664 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.60 41.0 4.05e-01 83.9% 66.2%
3518895 391.1.2.9 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related › Fn1_2 0.60 49.0 4.25e-01 91.9% 89.0%
4312419 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.60 42.0 2.82e-01 72.6% 81.3%
3687350 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 43.0 4.58e-01 75.8% 92.7%
3989574 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 37.0 3.38e-01 74.2% 44.7%
3737927 220.1.1.294 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF26663 0.59 49.0 4.08e-01 91.9% 63.6%
3630572 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.58 33.0 3.96e-01 71.0% 97.1%
5026824 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 39.0 3.78e-01 100.0% 61.4%
4391061 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.58 46.0 3.76e-01 88.7% 81.7%
3999534 391.1.2.9 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related › Fn1_2 0.58 36.0 4.32e-01 79.0% 100.0%
4190716 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.58 46.0 3.80e-01 88.7% 74.8%
5081762 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.57 42.0 2.53e-01 77.4% 90.1%
3963874 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.57 40.0 3.33e-01 75.8% 67.5%
5044391 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.57 39.0 4.29e-01 72.6% 94.0%
4236900 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.56 44.0 3.59e-01 88.7% 79.1%
3963647 2.8.1.0 ↗ beta barrels › OB-fold › mu transposases-C › mu transposases-C 0.56 39.0 3.68e-01 72.6% 65.3%
4281449 2.4.1.3 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2,OB_MalK 0.56 44.0 3.56e-01 88.7% 85.9%
5044394 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.56 39.0 4.28e-01 75.8% 100.0%
3233942 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.56 32.0 3.87e-01 72.6% 100.0%
5044389 4.26.1.0 ↗ beta barrels › SH3 › Chromatin protein Cren7 › Chromatin protein Cren7 0.55 39.0 4.26e-01 77.4% 94.0%
368907 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.55 38.0 3.09e-01 71.0% 55.5%
3231089 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.55 34.0 4.00e-01 72.6% 95.0%
4497740 325.1.7.3 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › Apocytochr_F_C 0.55 40.0 4.13e-01 79.0% 91.7%
5045206 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.55 42.0 2.56e-01 88.7% 72.0%
3792780 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.54 34.0 3.84e-01 93.5% 97.5%
4103327 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.54 46.0 3.77e-01 98.4% 81.3%
4606688 2.4.1.1 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE 0.54 39.0 3.76e-01 79.0% 69.3%
3505002 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.54 31.0 3.59e-01 72.6% 97.1%
4966092 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.54 46.0 3.72e-01 98.4% 73.4%
3338677 5.1.3.6 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1 0.53 46.0 2.89e-01 95.2% 87.4%
3792873 391.1.2.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related 0.53 33.0 3.79e-01 77.4% 97.5%
3969569 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.53 39.0 3.99e-01 79.0% 93.3%
3233227 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.53 46.0 4.07e-01 96.8% 71.1%
4417109 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.53 45.0 3.83e-01 98.4% 80.0%
5044392 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 37.0 3.92e-01 100.0% 85.5%
3893831 63.1.1.3 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › PRKCSH 0.53 38.0 3.02e-01 80.6% 83.4%
1214742 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.52 41.0 3.47e-01 85.5% 56.7%
4237578 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.52 43.0 3.58e-01 95.2% 80.0%
4016874 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.52 41.0 2.71e-01 90.3% 69.7%
3928508 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.52 44.0 2.77e-01 98.4% 93.5%
4165211 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.52 43.0 3.35e-01 96.8% 83.4%
4967263 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.51 43.0 3.66e-01 98.4% 76.4%
3619860 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.51 32.0 3.69e-01 95.2% 97.5%
4998346 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.51 43.0 3.49e-01 98.4% 76.2%
3716765 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.51 43.0 2.54e-01 98.4% 80.3%