←Back to structures

NC_055769.1__YP_010098772.1__KNU13_gp72__00072

Bact-Vir

NC_055769.1__YP_010098772.1__KNU13_gp72__00072

Identity

Accession:
NC_055769 ↗
Kingdom:
phage

Quality

86.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Zierdtviridae› Gruunavirus› Gordonia_phage_Turuncu

TaxID: 2315610

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 2-39
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4i14A02 3.40.50.10990 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › GTP cyclohydrolase II 0.69 49.0 3.53e-01 100.0% 24.6%
4pj2A00 2.40.128.460 Mainly Beta › Beta Barrel › Lipocalin › Periplasmic lysozyme inhibitor of I-type lysozyme 0.66 50.0 3.63e-01 100.0% 28.1%
3gxwC00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.66 46.0 3.52e-01 100.0% 29.0%
2nlkA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.63 50.0 3.10e-01 100.0% 13.8%
2i79D00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.63 41.0 2.65e-01 84.2% 15.0%
4dloB01 4.10.1240.10 Few Secondary Structures › Irregular › Hormone receptor fold › GPCR, family 2, extracellular hormone receptor domain 0.63 46.0 4.11e-01 100.0% 51.5%
3kxtA00 2.30.30.610 Mainly Beta › Roll › SH3 type barrels. › Chromatin protein Cren7 0.62 46.0 4.19e-01 100.0% 58.9%
1ut7B01 2.170.150.80 Mainly Beta › Beta Complex › Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A › NAC domain 0.60 47.0 3.49e-01 100.0% 32.8%
3pnrA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.60 48.0 3.04e-01 100.0% 17.5%
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.59 43.0 3.75e-01 100.0% 47.8%
2ia7A00 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.59 45.0 3.42e-01 100.0% 31.5%
3l4gC04 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 43.0 2.60e-01 100.0% 11.7%
1iz6A01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.57 40.0 3.61e-01 100.0% 47.8%
1gpqB00 3.40.1420.10 Alpha Beta › 3-Layer(aba) Sandwich › Inhibitor of vertebrate lysozyme, Ivy › Inhibitor of vertebrate lysozyme 0.57 41.0 3.04e-01 100.0% 25.8%
2uvaG07 3.30.1120.100 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.57 41.0 2.89e-01 94.7% 22.1%
2hv2A01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 38.0 2.98e-01 73.7% 28.4%
3q31A00 3.10.200.10 Alpha Beta › Roll › Carbonic Anhydrase II › Alpha carbonic anhydrase 0.56 45.0 2.85e-01 100.0% 16.1%
4lgvD02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.55 40.0 2.52e-01 97.4% 11.7%
3k8aB00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 40.0 3.25e-01 100.0% 43.7%
4xfwA00 3.10.200.10 Alpha Beta › Roll › Carbonic Anhydrase II › Alpha carbonic anhydrase 0.55 45.0 2.85e-01 100.0% 16.8%
2k50A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 42.0 3.26e-01 100.0% 35.6%
8aimG01 3.10.450.20 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Bacteriophage PBS2, uracil-glycosylase inhibitor 0.54 43.0 3.56e-01 100.0% 49.4%
6xw5A01 2.40.510.10 Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses 0.53 43.0 2.89e-01 100.0% 52.0%
2i52B00 3.30.1300.20 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 7,8-dihydroneopterin aldolase (MptD) 0.53 38.0 2.92e-01 100.0% 26.7%
2o95B00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.53 42.0 2.82e-01 100.0% 20.5%
1ul7A00 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.53 38.0 3.11e-01 97.4% 35.3%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.53 40.0 2.58e-01 97.4% 68.2%
1ei5A03 2.40.128.50 Mainly Beta › Beta Barrel › Lipocalin › 0.53 39.0 3.18e-01 100.0% 36.3%
4b0eD00 3.10.20.410 Alpha Beta › Roll › Ubiquitin-like (UB roll) › PapC, N-terminal domain 0.53 40.0 3.12e-01 100.0% 36.0%
1ut9A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 39.0 3.16e-01 100.0% 38.8%
3butA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 38.0 2.94e-01 100.0% 56.0%
2qkdA01 2.20.25.420 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ZPR1, zinc finger domain 0.52 38.0 3.62e-01 100.0% 66.7%
4xiwC00 3.10.200.10 Alpha Beta › Roll › Carbonic Anhydrase II › Alpha carbonic anhydrase 0.52 40.0 2.57e-01 100.0% 15.9%
2i00C01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 40.0 2.85e-01 100.0% 52.1%
7q5yB01 3.30.460.80 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › NADH:ubiquinone oxidoreductase Nqo5 subunit 0.51 37.0 2.89e-01 100.0% 28.3%
4aghA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.51 34.0 3.01e-01 100.0% 38.7%
6fu4A01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.51 35.0 2.59e-01 100.0% 22.1%
3we5A00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.51 44.0 3.03e-01 100.0% 27.0%
3rhtA00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.51 37.0 2.45e-01 97.4% 18.3%
2yfsA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.51 35.0 2.11e-01 100.0% 12.0%
7r97A02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.50 40.0 3.50e-01 100.0% 64.7%
2euiA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.50 38.0 2.69e-01 92.1% 25.0%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3251342 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.68 54.0 3.91e-01 100.0% 30.0%
3412668 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.68 54.0 3.92e-01 100.0% 30.0%
4522298 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 49.0 4.91e-01 100.0% 85.0%
3670792 243.3.1.67 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › Phytochelatin_C 0.65 49.0 4.33e-01 100.0% 53.8%
4962355 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.64 50.0 3.81e-01 100.0% 80.9%
3415002 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 49.0 4.05e-01 92.1% 84.8%
3948467 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.62 47.0 4.13e-01 100.0% 53.8%
5028774 206.1.3.21 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.61 45.0 2.95e-01 100.0% 17.3%
3935168 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.61 41.0 2.49e-01 100.0% 8.7%
4077367 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.61 46.0 4.07e-01 100.0% 53.8%
3505947 4.25.1.2 ↗ beta barrels › SH3 › Auxin response factor dimerization domain and ancillary domain › Auxin response factor dimerization domain and ancillary domain › BRWD_AD 0.61 47.0 3.48e-01 100.0% 30.0%
3687369 4.1.1.225 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7025 0.59 47.0 3.64e-01 100.0% 38.0%
4024738 220.1.1.243 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF30062 0.58 46.0 3.53e-01 100.0% 37.1%
5013094 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.58 45.0 3.07e-01 100.0% 21.2%
3419350 1.1.1.19 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Pol_BBD 0.58 43.0 2.76e-01 92.1% 15.3%
5047301 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.57 42.0 3.54e-01 100.0% 53.3%
3266842 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.57 43.0 3.26e-01 100.0% 31.2%
3433407 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.57 39.0 2.84e-01 94.7% 21.5%
3217507 243.1.1.98 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF5382_C 0.56 41.0 3.25e-01 100.0% 34.2%
4882461 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.56 42.0 3.32e-01 97.4% 83.0%
3577471 221.13.1.0 ↗ a+b two layers › beta-Grasp › Mitochondrial calcium uniporter N-terminal domain › Mitochondrial calcium uniporter N-terminal domain 0.55 42.0 3.13e-01 100.0% 48.5%
5062717 283.2.1.1 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › GPW_gp25 0.54 40.0 3.14e-01 100.0% 30.4%
5049449 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.54 37.0 3.62e-01 100.0% 62.0%
3224227 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.54 41.0 2.58e-01 97.4% 38.5%
3472467 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.54 39.0 3.27e-01 100.0% 42.7%
3821077 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.53 42.0 2.51e-01 100.0% 70.1%
1555393 2.1.1.4 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_S17 0.53 40.0 2.95e-01 92.1% 27.7%
4943340 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.53 39.0 3.32e-01 100.0% 43.5%
3931232 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 37.0 2.94e-01 100.0% 45.6%
5046317 213.1.1.29 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_9 0.52 40.0 2.93e-01 97.4% 43.8%
3217156 243.1.1.46 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF5382 0.52 37.0 2.77e-01 100.0% 25.0%
5055710 4985.1.1.0 ↗ few secondary structure elements › DPY module › DPY module › DPY module 0.52 37.0 3.70e-01 100.0% 85.0%
4839875 1061.1.1.1 ↗ a+b two layers › gp120 inner domain › gp120 inner domain › gp120 inner domain › GP120 0.52 37.0 3.56e-01 97.4% 67.2%
3292852 4086.1.1.1 ↗ a+b two layers › AMPKBI-like › AMPKBI-like › AMPKBI-like › AMPKBI 0.52 37.0 3.01e-01 100.0% 33.7%
4807995 4.1.1.314 ↗ beta barrels › SH3 › SH3 › SH3 › KOW, Ribosomal_uL24m-like 0.52 37.0 2.39e-01 92.1% 32.3%
5051718 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 38.0 2.26e-01 100.0% 9.2%
3998224 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.51 43.0 2.94e-01 100.0% 51.0%
3232194 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.51 43.0 2.72e-01 100.0% 34.4%
4820757 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.51 37.0 2.98e-01 100.0% 31.8%
3555586 4.1.1.19 ↗ beta barrels › SH3 › SH3 › SH3 › LSM 0.51 37.0 3.04e-01 94.7% 46.3%
3645476 295.1.1.1 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PC4 0.50 37.0 3.00e-01 100.0% 33.0%