←Back to structures

MH925093.1__QAY02061.1__VspDsh1_39__00038

Bact-Vir

MH925093.1__QAY02061.1__VspDsh1_39__00038

Identity

Accession:
MH925093 ↗
Kingdom:
phage

Quality

92.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_VspDsh_1

TaxID: 2484248

Cluster

View cluster (9 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 medium residues 1-191
PDB
Domain cluster: rep: NC_005178.1__NP_938253.1__D3112p46__00046__D2-182
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1z94B00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.60 36.0 4.09e-01 93.7% 78.3%
2kd2A01 2.40.128.180 Mainly Beta › Beta Barrel › Lipocalin › 0.59 25.0 3.55e-01 88.5% 83.3%
2kf2A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.59 36.0 3.80e-01 97.4% 66.5%
2fpnA01 3.30.2030.10 Alpha Beta › 2-Layer Sandwich › TBP-like › YwmB-like 0.59 33.0 3.80e-01 93.2% 72.9%
2ns9A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.58 35.0 3.95e-01 97.9% 75.7%
3w9kA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 32.0 3.72e-01 74.9% 74.8%
3eliA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 36.0 4.08e-01 92.7% 81.9%
2d4rA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 35.0 3.98e-01 98.4% 80.1%
2l8oA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 33.0 3.78e-01 98.4% 76.4%
1pbyA02 2.40.128.120 Mainly Beta › Beta Barrel › Lipocalin › Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 0.54 29.0 3.73e-01 91.1% 90.6%
4akrA02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.54 38.0 4.27e-01 91.6% 93.9%
3aa0B02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.52 38.0 4.16e-01 92.1% 91.6%
7knlA01 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.52 32.0 3.89e-01 94.8% 99.1%
3ijtB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.52 31.0 3.49e-01 92.7% 76.2%
3mswA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.52 34.0 3.89e-01 88.5% 89.9%
3tfzB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 35.0 3.74e-01 76.4% 79.4%
3hdjA01 3.30.1780.10 Alpha Beta › 2-Layer Sandwich › ornithine cyclodeaminase, domain 1 › ornithine cyclodeaminase, domain 1 0.51 33.0 3.79e-01 97.4% 87.9%
1o8vA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.51 28.0 3.20e-01 89.5% 71.4%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5038083 331.9.1.0 ↗ a+b two layers › TBP-like › Subdomain of clathrin and coatomer appendage domain › Subdomain of clathrin and coatomer appendage domain 0.65 33.0 4.09e-01 80.1% 76.6%
3282719 331.3.1.11 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc2 0.60 37.0 3.92e-01 97.9% 68.5%
4330244 331.3.1.5 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc 0.59 32.0 4.08e-01 77.5% 90.8%
3272624 4210.1.1.1 ↗ a+b two layers › WGR domain › WGR domain › WGR domain › WGR 0.59 28.0 3.36e-01 96.3% 64.6%
6333 331.3.1.7 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › COXG 0.58 35.0 3.95e-01 97.9% 76.2%
5074212 331.10.2.0 ↗ a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.57 30.0 3.88e-01 84.3% 87.3%
3706858 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.56 39.0 4.55e-01 93.2% 100.0%
4227522 330.6.1.0 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain 0.55 28.0 3.71e-01 82.7% 89.5%
3685749 4051.1.1.2 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F-actin_cap_A 0.54 36.0 4.01e-01 95.3% 84.7%
3299865 331.3.1.17 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › VASt 0.54 37.0 3.97e-01 97.9% 80.6%
3660463 331.3.1.17 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › VASt 0.54 37.0 3.91e-01 97.9% 76.6%
4403206 4051.1.1.2 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F-actin_cap_A 0.53 35.0 3.81e-01 70.2% 79.4%
4466411 4051.1.1.2 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F-actin_cap_A 0.53 36.0 3.77e-01 94.2% 73.7%
3628966 331.3.1.3 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › START 0.52 37.0 3.56e-01 87.4% 61.8%
3794870 216.1.1.2 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › Autophagy_act_C 0.52 37.0 4.05e-01 73.3% 92.5%
3230598 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.51 37.0 4.13e-01 73.3% 94.7%
3782223 331.3.1.17 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › VASt 0.51 35.0 3.33e-01 97.4% 57.8%
3897847 216.1.1.2 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › Autophagy_act_C 0.51 36.0 3.88e-01 73.3% 92.3%
3234900 331.3.1.3 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › START 0.50 36.0 3.37e-01 76.4% 58.7%
D2 medium residues 192-274
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1n08A00 2.40.30.30 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like 0.56 40.0 3.36e-01 77.1% 50.0%
3r2uB01 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.52 44.0 3.24e-01 100.0% 83.3%
4ywzB00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.50 42.0 3.60e-01 97.6% 82.2%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4316228 1.1.12.1 ↗ beta barrels › cradle loop barrel › RIFT-related › barrel domain in QueA-like proteins › Queuosine_synth 0.64 45.0 4.21e-01 86.7% 58.1%
3979944 391.1.1.6 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › DUF1496 0.63 32.0 4.07e-01 85.5% 88.9%
3818230 376.1.2.16 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1-like_CT 0.58 34.0 3.83e-01 85.5% 75.4%
4035765 6043.2.1.0 ↗ a+b two layers › yfeY-like › Teichoic acid transporter subunit TagH C-terminal domain › Teichoic acid transporter subunit TagH C-terminal domain 0.56 41.0 3.60e-01 78.3% 98.4%
4154363 1.1.12.1 ↗ beta barrels › cradle loop barrel › RIFT-related › barrel domain in QueA-like proteins › Queuosine_synth 0.55 44.0 3.82e-01 86.7% 58.5%
5045021 239.1.1.0 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like 0.52 35.0 3.93e-01 85.5% 95.0%
3956024 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 45.0 3.27e-01 100.0% 82.1%
3251396 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 38.0 3.58e-01 86.7% 64.8%