←Back to structures

NC_073468.1__YP_010755118.1__QEH42_gp087__00087

Bact-Vir

NC_073468.1__YP_010755118.1__QEH42_gp087__00087

Identity

Accession:
NC_073468 ↗
Kingdom:
phage

Quality

86.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pumpernickelvirus› Microbacterium_phage_Pumpernickel

TaxID: 2885983

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 8-50_73-223
PDB
Domain cluster: rep: KX365748.1__ANY29585.1__X__00020__D206-385
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3gs9A01 6.20.110.10 Special › Other non-globular › Thrombin, subunit H › 0.69 30.0 4.57e-01 75.3% 100.0%
1kiaA01 3.30.46.10 Alpha Beta › 2-Layer Sandwich › Glycine N-methyltransferase; chain A, domain 1 › Glycine N-methyltransferase, chain A, domain 1 0.68 21.0 3.33e-01 76.3% 66.3%
5ejlA02 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.66 36.0 4.40e-01 90.7% 81.5%
4w64B00 2.30.110.20 Mainly Beta › Roll › Pnp Oxidase; Chain A › Hcp1-like 0.63 44.0 4.81e-01 91.8% 86.3%
1hi9A02 3.30.1360.130 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Dipeptide transport protein 0.61 24.0 3.92e-01 95.4% 96.1%
3eaaA00 2.30.110.20 Mainly Beta › Roll › Pnp Oxidase; Chain A › Hcp1-like 0.61 44.0 4.84e-01 92.8% 89.5%
4divV01 2.40.30.200 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.59 39.0 4.64e-01 90.2% 94.9%
3n0vA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.58 24.0 3.51e-01 75.3% 85.7%
2b9lA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.57 31.0 3.42e-01 92.8% 62.4%
3lnnA02 2.40.30.170 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain 0.57 29.0 3.88e-01 86.6% 97.8%
4qjvA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.56 25.0 3.51e-01 85.1% 87.6%
2nyiA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.54 22.0 3.11e-01 70.6% 77.8%
1c16A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 26.0 3.51e-01 83.5% 89.7%
2apoA03 3.30.70.3190 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 24.0 3.27e-01 78.9% 83.7%
3ue2A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.52 24.0 3.28e-01 77.8% 89.8%
1q8bA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 23.0 3.18e-01 75.3% 86.0%
1nvmB02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.50 30.0 3.36e-01 90.2% 73.4%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4140243 1.1.5.82 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF2001 0.79 46.0 5.97e-01 92.3% 98.3%
4032554 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.72 59.0 6.41e-01 97.9% 100.0%
3943316 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.72 56.0 6.13e-01 94.3% 96.9%
5040331 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.71 52.0 5.94e-01 93.8% 100.0%
5040332 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.70 41.0 5.27e-01 93.8% 97.4%
4960006 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.69 38.0 4.99e-01 91.8% 95.4%
185291 1.1.13.20 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Prophage_tailD1 0.69 31.0 4.63e-01 75.8% 100.0%
3943282 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.68 37.0 4.61e-01 91.2% 84.2%
4009489 1.1.5.23 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › T6SS_HCP 0.67 48.0 5.32e-01 92.3% 90.3%
3943691 1.1.13.5 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_GPD 0.66 34.0 4.57e-01 77.3% 97.9%
2101633 1.1.13.1 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_tube 0.65 49.0 5.26e-01 92.3% 89.8%
3942828 1.1.13.39 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › KPP10_Orf10 0.63 46.0 5.21e-01 93.3% 99.3%
136185 1.1.5.23 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › T6SS_HCP 0.61 44.0 4.84e-01 92.8% 89.5%
3969384 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.61 45.0 4.92e-01 92.8% 92.5%
4034209 1.1.13.4 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Sipho_tail 0.60 41.0 4.88e-01 77.3% 100.0%
3823591 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.59 31.0 4.09e-01 83.5% 94.0%
5038472 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.56 33.0 4.22e-01 85.6% 100.0%
5057180 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 26.0 3.74e-01 83.0% 94.4%
5037829 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.55 23.0 3.21e-01 73.7% 75.0%
3679489 11.2.1.37 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › DUF6598 0.55 26.0 3.19e-01 92.3% 66.4%
3721754 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.55 26.0 3.22e-01 71.1% 69.2%
3483013 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.54 25.0 3.12e-01 76.3% 69.2%
3949940 319.1.1.4 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › ArsA_HSP20 0.53 25.0 3.59e-01 73.2% 98.8%
3618913 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 26.0 3.54e-01 93.8% 90.0%
5041091 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 27.0 3.45e-01 85.1% 84.3%
4149046 243.3.1.60 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF5385 0.51 23.0 3.28e-01 89.7% 87.8%
3564603 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 24.0 3.19e-01 70.1% 84.2%
3807080 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 34.0 3.52e-01 93.8% 69.7%
5043492 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.51 24.0 3.14e-01 76.8% 80.8%
4401956 304.25.1.0 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain 0.51 24.0 3.31e-01 75.3% 89.5%
D2 high residues 227-307
PDB
Domain cluster: rep: OK040790.1__UDL15888.1__SEA_PUMPERNICKEL_97__00097__D598-675