←Back to structures

JX238501.3__AGB62643.1__X__00197

Bact-Vir

JX238501.3__AGB62643.1__X__00197

Identity

Accession:
JX238501 ↗
Kingdom:
phage

Quality

87.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Herelleviridae› Agatevirus› Bacillus_phage_phiAGATE

TaxID: 1204533

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 3-67
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ga8A00 3.10.20.860 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.67 57.0 5.73e-01 98.5% 100.0%
3bzwF00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.64 44.0 2.97e-01 70.8% 70.4%
1kcgC00 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.60 43.0 3.24e-01 75.4% 85.9%
3aonA00 1.10.287.3240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 47.0 3.40e-01 87.7% 40.4%
5vmzA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.58 31.0 3.63e-01 86.2% 79.5%
6zzmA01 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.57 42.0 2.91e-01 78.5% 75.0%
4indA01 2.60.120.1320 Mainly Beta › Sandwich › Jelly Rolls › 0.56 40.0 3.07e-01 75.4% 93.2%
1p1lA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 40.0 3.48e-01 76.9% 60.8%
1t7vA01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.55 41.0 3.07e-01 81.5% 41.6%
3e35A01 3.40.50.10900 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › PAC-like subunit 0.55 41.0 2.83e-01 80.0% 57.3%
4fnfA00 2.40.50.50 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 41.0 3.60e-01 84.6% 91.8%
3qjlA02 3.30.70.1900 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 35.0 2.82e-01 78.5% 37.0%
1vw3C01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.52 40.0 3.24e-01 84.6% 48.1%
1s68A02 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.52 38.0 3.28e-01 81.5% 80.5%
3p9aF00 1.10.132.80 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.52 42.0 3.36e-01 89.2% 73.9%
6gp1A00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.52 35.0 3.58e-01 86.2% 70.8%
6l4lA02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.51 38.0 3.03e-01 80.0% 61.8%
3wlvA00 3.10.270.10 Alpha Beta › Roll › Urate Oxidase › Urate Oxidase; 0.51 40.0 2.68e-01 90.8% 46.2%
2wozA00 2.120.10.80 Mainly Beta › 6 Propeller › Neuraminidase › Kelch-type beta propeller 0.50 39.0 2.54e-01 84.6% 84.7%
6dgiA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.50 37.0 2.97e-01 81.5% 50.7%
2q07A02 3.10.450.90 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › ArcTGT, C2 domain 0.50 37.0 3.76e-01 81.5% 95.4%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4959386 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.87 64.0 7.17e-01 92.3% 100.0%
4992532 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.83 70.0 7.26e-01 92.3% 98.3%
4947479 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.81 59.0 6.55e-01 81.5% 100.0%
4968647 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.80 54.0 6.11e-01 70.8% 100.0%
4992806 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.79 62.0 6.67e-01 89.2% 100.0%
4968137 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.77 60.0 6.45e-01 93.8% 100.0%
4968450 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.77 57.0 6.09e-01 87.7% 94.5%
4661366 375.1.1.271 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › YokU 0.77 68.0 6.51e-01 100.0% 90.7%
4993925 375.1.1.338 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF7479 0.76 55.0 5.96e-01 86.2% 100.0%
5030510 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.74 53.0 5.77e-01 84.6% 100.0%
5061538 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.70 53.0 5.60e-01 89.2% 100.0%
5031242 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.68 55.0 5.68e-01 96.9% 100.0%
5031701 375.1.1.55 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › MqsA_antitoxin 0.68 57.0 5.76e-01 93.8% 100.0%
5081200 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.67 52.0 5.40e-01 98.5% 96.7%
3977240 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.66 46.0 4.68e-01 73.8% 81.5%
380878 375.1.1.55 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › MqsA_antitoxin 0.66 56.0 5.48e-01 98.5% 95.7%
4966283 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.65 56.0 5.62e-01 96.9% 95.4%
5071836 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.64 43.0 3.87e-01 84.6% 50.0%
3471203 2011.1.1.8 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.61 46.0 2.95e-01 81.5% 51.0%
3459267 2011.1.1.8 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.61 44.0 2.84e-01 78.5% 47.8%
4974958 2004.1.2.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › PEP carboxykinase catalytic C-terminal domain 0.60 44.0 2.70e-01 76.9% 51.7%
3809314 376.1.2.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain 0.59 40.0 4.44e-01 70.8% 98.0%
3861324 386.1.1.1 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2 0.58 30.0 3.35e-01 83.1% 62.0%
3263073 2492.1.1.2 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › JAB 0.57 40.0 2.78e-01 76.9% 20.5%
4991381 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 42.0 3.55e-01 81.5% 47.9%
4971344 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.57 41.0 4.54e-01 80.0% 100.0%
3261672 3696.1.1.0 ↗ a+b two layers › DNA helicase UvsW N-terminal a+b domain-related › DNA helicase UvsW N-terminal a+b domain-related › DNA helicase UvsW N-terminal a+b domain-related 0.56 31.0 2.81e-01 96.9% 38.9%
3833792 376.1.2.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain 0.56 39.0 3.56e-01 76.9% 57.9%
3990856 304.112.1.0 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.55 42.0 3.33e-01 84.6% 40.7%
5052865 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.55 38.0 3.44e-01 72.3% 95.3%
3194310 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.55 47.0 3.32e-01 95.4% 44.3%
4376968 865.1.1.1 ↗ beta complex topology › PheT/TilS domain › PheT/TilS domain › PheT/TilS domain › B3_4 0.54 42.0 3.18e-01 89.2% 72.8%
4076048 2492.1.1.4 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.53 38.0 2.68e-01 75.4% 28.6%
3612874 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.53 46.0 2.98e-01 95.4% 51.1%
3801858 252.1.1.0 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD 0.52 32.0 3.37e-01 70.8% 68.3%
3599368 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.52 45.0 3.00e-01 95.4% 57.2%
None — 0.50 40.0 2.72e-01 95.4% 66.4%
5011928 206.1.3.7 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATP-grasp 0.50 38.0 2.53e-01 83.1% 60.1%