←Back to structures

NC_042056.1__YP_009616989.1__FDI85_gp212__00063

Bact-Vir

NC_042056.1__YP_009616989.1__FDI85_gp212__00063

Identity

Accession:
NC_042056 ↗
Kingdom:
phage

Quality

77.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Machinavirus› Erwinia_phage_Machina

TaxID: 1883375

Cluster

View cluster (3 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 46-141
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.72 42.0 4.06e-01 92.7% 51.9%
3d31A03 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.71 32.0 3.71e-01 86.5% 56.3%
4bf3A00 2.30.31.50 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Borrelia outer surface protein E/F 0.62 50.0 4.50e-01 87.5% 72.2%
5xpyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 39.0 3.82e-01 100.0% 59.3%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.60 52.0 4.59e-01 96.9% 69.3%
5t1dB00 3.10.390.20 Alpha Beta › Roll › SAND domain › Viral glycoprotein L 0.59 35.0 3.55e-01 97.9% 57.6%
4upiA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.59 46.0 2.96e-01 85.4% 41.7%
2nvnA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.59 50.0 4.65e-01 96.9% 75.0%
2ffgA00 3.30.720.20 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Protein of unknown function DUF1797 0.58 42.0 4.52e-01 81.2% 91.3%
3qijB03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 35.0 3.67e-01 97.9% 67.4%
2da0A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 38.0 3.57e-01 77.1% 57.9%
5jozB02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.56 42.0 3.36e-01 81.2% 67.8%
4nswA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 37.0 3.56e-01 95.8% 59.6%
7byjA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 37.0 3.73e-01 94.8% 68.4%
1zc3B00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 39.0 3.78e-01 100.0% 65.1%
4hhvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 37.0 3.62e-01 99.0% 63.1%
2rgnB02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 39.0 3.66e-01 100.0% 58.5%
1ntyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 35.0 3.24e-01 94.8% 50.8%
3k25A00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.53 38.0 2.74e-01 76.0% 75.7%
3pg7A02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 37.0 3.57e-01 100.0% 63.6%
2zdiC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 41.0 3.55e-01 91.7% 54.1%
1vpkA02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.52 44.0 4.03e-01 94.8% 69.5%
1ukfA00 3.90.70.20 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.52 42.0 3.38e-01 87.5% 87.2%
3gvzA00 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.52 42.0 3.15e-01 90.6% 76.2%
4yt3A00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.51 44.0 3.05e-01 100.0% 36.9%
3qwmA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 37.0 3.42e-01 100.0% 58.3%
3ml4A02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 32.0 3.21e-01 99.0% 61.0%
4r7rA00 3.30.1490.410 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Uncharacterised protein PF16224, DUF4883 0.50 40.0 3.75e-01 87.5% 87.7%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4951344 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.71 32.0 3.06e-01 86.5% 34.8%
4963673 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.65 37.0 3.59e-01 72.9% 49.1%
5066631 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.63 36.0 3.53e-01 72.9% 50.5%
4974630 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.61 34.0 3.43e-01 71.9% 51.0%
3556135 220.1.1.49 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Carm_PH 0.61 40.0 3.43e-01 100.0% 42.7%
5014255 220.1.1.87 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_3 0.59 38.0 3.48e-01 100.0% 46.7%
4638994 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.58 39.0 3.71e-01 72.9% 57.4%
6667 4221.1.1.1 ↗ a+b two layers › YkuJ-like › YkuJ-like › YkuJ-like › DUF1797 0.58 42.0 4.56e-01 81.2% 93.6%
3388849 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 39.0 3.43e-01 100.0% 46.9%
3219284 2484.1.1.190 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FBA_2 0.56 39.0 2.89e-01 90.6% 26.0%
3869833 109.4.1.3457 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HPS3_N, HPS3_C 0.55 40.0 2.97e-01 76.0% 85.1%
3697524 9.2.1.7 ↗ beta barrels › Lipocalins/Streptavidin › Avidin/Streptavidin › Avidin/Streptavidin › PF30970 0.54 39.0 4.03e-01 80.2% 80.0%
3233897 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 37.0 3.53e-01 90.6% 58.3%
3418985 10.1.1.11 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Glyco_hydro_16 0.53 43.0 3.49e-01 89.6% 72.3%
4950191 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.53 37.0 3.44e-01 72.9% 100.0%
3621277 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.53 40.0 3.46e-01 100.0% 51.0%
None — 0.52 39.0 2.58e-01 79.2% 21.3%
3290349 3844.2.1.1 ↗ a+b two layers › hydrogenase expression protein-like › MybT EspG5 chaperone › MybT EspG5 chaperone › ESX-1_EspG 0.51 41.0 3.07e-01 87.5% 69.0%
4057537 227.1.1.1 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.50 44.0 4.05e-01 96.9% 84.0%
5078664 4018.1.1.0 ↗ a+b two layers › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases 0.50 35.0 3.16e-01 72.9% 79.3%