←Back to structures

NC_053505.1__YP_010012645.1__J4T94_gp122__00059

Bact-Vir

NC_053505.1__YP_010012645.1__J4T94_gp122__00059

Identity

Accession:
NC_053505 ↗
Kingdom:
phage

Quality

90.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vilmaviridae› Lumosvirus› Mycobacterium_phage_Krypton555

TaxID: 2015885

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 2-55
PDB
Domain cluster: representative
CATH (57)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2x4jA01 2.30.30.600 Mainly Beta › Roll › SH3 type barrels. › 0.77 61.0 4.98e-01 98.1% 47.1%
2k57A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.73 61.0 6.14e-01 98.1% 96.4%
1y96A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.72 62.0 5.36e-01 100.0% 67.4%
1lqlA01 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.71 36.0 4.35e-01 77.8% 92.3%
1kq1H00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.71 54.0 5.16e-01 96.3% 71.2%
4xtvB02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.71 54.0 5.60e-01 98.1% 95.8%
2ra2B00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.70 60.0 5.91e-01 100.0% 98.3%
1u1sA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.69 54.0 5.13e-01 98.1% 72.7%
2jrbA00 3.30.250.20 Alpha Beta › 2-Layer Sandwich › Rec A Protein; domain 2 › L1 transposable element, C-terminal domain 0.68 40.0 3.82e-01 83.3% 49.2%
1y96D00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.68 56.0 5.00e-01 98.1% 68.7%
2fb7A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.68 57.0 5.09e-01 98.1% 88.7%
4iauA01 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.68 43.0 3.85e-01 100.0% 44.9%
2e5yA01 2.60.15.10 Mainly Beta › Sandwich › ATP Synthase; domain 1 › F0F1 ATP synthase delta/epsilon subunit, N-terminal 0.67 58.0 5.01e-01 100.0% 81.8%
4x9cD00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.67 51.0 4.99e-01 94.4% 78.3%
4k17B01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.65 49.0 4.02e-01 85.2% 78.4%
2oqbA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.65 51.0 4.12e-01 87.0% 92.6%
2hldH01 2.60.15.10 Mainly Beta › Sandwich › ATP Synthase; domain 1 › F0F1 ATP synthase delta/epsilon subunit, N-terminal 0.64 53.0 4.63e-01 94.4% 84.5%
7afrX02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.62 49.0 4.83e-01 96.3% 85.0%
1sg5A01 2.30.30.400 Mainly Beta › Roll › SH3 type barrels. › Rof-like 0.62 49.0 4.53e-01 96.3% 67.5%
2krsA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.61 45.0 4.42e-01 81.5% 100.0%
3hrsA02 2.30.30.90 Mainly Beta › Roll › SH3 type barrels. › Ferrous iron transport protein A (FeoA) 0.61 51.0 4.67e-01 100.0% 84.2%
1ex4B02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.61 46.0 4.56e-01 96.3% 81.4%
2avtB01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.61 47.0 3.35e-01 87.0% 64.5%
6uzjA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.59 47.0 4.51e-01 90.7% 93.7%
2hzmA02 2.20.140.20 Mainly Beta › Single Sheet › q64v53_bacfr protein fold › 0.58 51.0 4.44e-01 100.0% 98.8%
2d9tA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.57 45.0 4.63e-01 94.4% 98.0%
1uwvA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 39.0 3.55e-01 72.2% 75.3%
2z8lA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.57 42.0 3.44e-01 100.0% 39.3%
1ib8A02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.56 45.0 4.33e-01 96.3% 82.1%
3htxA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 44.0 3.97e-01 87.0% 84.2%
1mkeA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 44.0 3.46e-01 98.1% 90.3%
2hqvA00 3.40.1570.10 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains 0.55 47.0 3.42e-01 100.0% 46.5%
2i51B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 47.0 3.27e-01 100.0% 28.8%
3ap9A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.54 46.0 3.43e-01 100.0% 76.8%
6n44A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.54 45.0 3.50e-01 100.0% 79.1%
2iz4A01 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.54 35.0 3.72e-01 79.6% 75.5%
2wsuB02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.54 45.0 3.44e-01 100.0% 81.9%
2fhdA02 2.30.30.810 Mainly Beta › Roll › SH3 type barrels. › 0.54 43.0 4.03e-01 96.3% 91.7%
5o99A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.53 42.0 4.16e-01 98.1% 95.0%
1r75A00 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 46.0 3.70e-01 100.0% 52.7%
4dguA02 2.60.40.2670 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 39.0 3.30e-01 83.3% 92.3%
1e2tA02 3.30.1120.150 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.53 39.0 3.41e-01 94.4% 51.2%
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.53 41.0 4.04e-01 98.1% 84.6%
4iimA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.53 41.0 4.07e-01 94.4% 100.0%
7cfdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.52 39.0 3.66e-01 96.3% 65.8%
3o0wA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 43.0 2.92e-01 100.0% 50.4%
1z6hA00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.52 39.0 3.66e-01 87.0% 79.2%
3h8zA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.52 40.0 3.89e-01 98.1% 76.6%
1bdoA00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.51 38.0 3.49e-01 85.2% 82.5%
3u50C01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 41.0 3.29e-01 96.3% 97.6%
3ss3C02 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 38.0 2.42e-01 87.0% 14.3%
8enbA01 2.10.90.10 Mainly Beta › Ribbon › Cystine Knot Cytokines, subunit B › Cystine-knot cytokines 0.51 36.0 3.09e-01 74.1% 81.9%
4epcA02 2.30.30.170 Mainly Beta › Roll › SH3 type barrels. › 0.51 41.0 3.83e-01 94.4% 84.5%
2eqmA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 39.0 3.97e-01 90.7% 92.5%
1igqB00 2.30.30.150 Mainly Beta › Roll › SH3 type barrels. › KorB, C-terminal domain 0.51 38.0 3.85e-01 100.0% 86.0%
1mhnA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 40.0 3.95e-01 98.1% 86.4%
3uv0B00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.51 41.0 3.48e-01 96.3% 100.0%
ECOD (80)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4995694 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.84 75.0 7.50e-01 98.1% 96.4%
25624 4.1.1.45 ↗ beta barrels › SH3 › SH3 › SH3 › DUF903 0.76 63.0 6.42e-01 96.3% 100.0%
4118226 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.75 65.0 5.99e-01 100.0% 75.7%
4359892 4.1.1.96 ↗ beta barrels › SH3 › SH3 › SH3 › Hfq 0.75 59.0 5.27e-01 98.1% 60.0%
3968342 4.1.1.45 ↗ beta barrels › SH3 › SH3 › SH3 › DUF903 0.75 63.0 6.34e-01 96.3% 98.1%
4299932 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.74 64.0 6.10e-01 100.0% 81.5%
5063433 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.74 58.0 6.02e-01 98.1% 96.0%
4940673 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.72 57.0 5.62e-01 100.0% 81.7%
4069793 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.72 63.0 5.81e-01 100.0% 77.1%
3712219 4.1.1.19 ↗ beta barrels › SH3 › SH3 › SH3 › LSM 0.72 61.0 5.83e-01 100.0% 81.5%
4953913 4.1.1.19 ↗ beta barrels › SH3 › SH3 › SH3 › LSM 0.72 57.0 5.61e-01 98.1% 81.7%
4065466 220.1.1.150 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF986 0.71 55.0 4.86e-01 85.2% 86.3%
4302032 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.71 61.0 5.76e-01 100.0% 81.5%
1263519 4.1.1.96 ↗ beta barrels › SH3 › SH3 › SH3 › Hfq 0.71 54.0 5.27e-01 96.3% 75.8%
4429329 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.71 59.0 5.60e-01 96.3% 78.5%
4347922 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.71 58.0 5.66e-01 94.4% 83.3%
4499953 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.71 55.0 5.41e-01 98.1% 80.0%
4660084 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.70 60.0 5.60e-01 100.0% 76.8%
5074749 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.70 55.0 5.12e-01 98.1% 68.6%
3979842 4.1.1.45 ↗ beta barrels › SH3 › SH3 › SH3 › DUF903 0.70 59.0 5.92e-01 100.0% 100.0%
4058174 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.70 56.0 5.33e-01 98.1% 76.9%
3755800 3338.2.1.0 ↗ a+b two layers › Fragilysin-3 prodomain-like › Type II secretion chaperone CpaB › Type II secretion chaperone CpaB 0.69 47.0 3.73e-01 70.4% 94.5%
4559371 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.69 59.0 5.69e-01 100.0% 85.7%
3786412 4.1.1.344 ↗ beta barrels › SH3 › SH3 › SH3 › PF31193 0.69 59.0 5.29e-01 100.0% 80.0%
4088209 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.69 59.0 5.58e-01 100.0% 81.5%
4033484 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.69 57.0 5.49e-01 96.3% 85.9%
4527355 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.68 58.0 5.44e-01 100.0% 78.3%
3602511 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.68 54.0 5.05e-01 96.3% 71.4%
4216845 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.68 57.0 5.24e-01 100.0% 72.6%
4476045 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.68 57.0 5.32e-01 100.0% 75.7%
4202176 220.1.1.123 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_SSH1-like_1st 0.67 54.0 3.81e-01 92.6% 53.7%
3036710 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 53.0 5.09e-01 94.4% 74.6%
4941512 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 52.0 4.87e-01 98.1% 68.6%
5033892 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 56.0 5.37e-01 100.0% 81.5%
5004476 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 53.0 5.11e-01 100.0% 76.9%
3598125 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 56.0 5.15e-01 100.0% 76.0%
4959077 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 55.0 5.27e-01 96.3% 100.0%
4185009 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.67 56.0 5.36e-01 100.0% 81.5%
3730011 4.1.1.17 ↗ beta barrels › SH3 › SH3 › SH3 › Ribosomal_L19 0.67 59.0 4.37e-01 100.0% 43.6%
4034320 4.1.1.398 ↗ beta barrels › SH3 › SH3 › SH3 › YolD 0.67 55.0 5.22e-01 98.1% 80.9%
1482194 4.1.1.96 ↗ beta barrels › SH3 › SH3 › SH3 › Hfq 0.67 51.0 4.99e-01 94.4% 78.3%
4226934 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.67 54.0 5.14e-01 94.4% 76.9%
4104821 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.66 55.0 5.06e-01 100.0% 70.7%
4124780 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.66 55.0 5.10e-01 100.0% 72.6%
4010681 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.66 55.0 4.72e-01 100.0% 56.8%
4118552 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.66 56.0 5.13e-01 100.0% 76.0%
4079197 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.66 54.0 4.76e-01 96.3% 61.2%
4122525 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.65 54.0 5.00e-01 100.0% 74.7%
4261362 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.65 55.0 5.14e-01 100.0% 77.1%
4139778 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.65 55.0 5.08e-01 100.0% 74.0%
4149821 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.65 51.0 4.97e-01 100.0% 80.0%
4342110 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.65 55.0 5.06e-01 100.0% 74.0%
3281271 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.65 54.0 4.70e-01 100.0% 64.4%
4574546 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.65 53.0 5.12e-01 98.1% 83.1%
3286662 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.65 54.0 4.53e-01 100.0% 53.0%
5053906 4.17.1.1 ↗ beta barrels › SH3 › GatD N-terminal domain-like › GatD N-terminal domain-like › GatD_N 0.64 55.0 5.36e-01 100.0% 91.7%
4286562 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.64 54.0 5.14e-01 100.0% 81.5%
3511375 4.1.1.349 ↗ beta barrels › SH3 › SH3 › SH3 › ROF 0.64 52.0 4.65e-01 98.1% 62.4%
4264671 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.64 53.0 4.80e-01 100.0% 67.5%
3987498 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.64 53.0 4.70e-01 100.0% 65.9%
5045214 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.63 52.0 4.94e-01 100.0% 78.6%
3586825 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.63 50.0 3.06e-01 87.0% 26.6%
4212091 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.63 52.0 5.02e-01 100.0% 81.5%
4505797 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.63 52.0 5.05e-01 100.0% 83.1%
3289944 4.1.1.323 ↗ beta barrels › SH3 › SH3 › SH3 › WYL 0.63 51.0 4.54e-01 100.0% 64.4%
3232582 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.63 52.0 4.50e-01 100.0% 63.2%
4269844 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.63 51.0 4.75e-01 96.3% 72.9%
4937731 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.63 50.0 4.85e-01 90.7% 80.0%
5077969 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.62 49.0 4.47e-01 96.3% 63.7%
3387119 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.62 50.0 4.39e-01 100.0% 58.9%
3593222 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 48.0 4.38e-01 98.1% 64.6%
4621153 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 50.0 4.94e-01 100.0% 91.7%
4942163 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 49.0 4.69e-01 100.0% 80.0%
5029655 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 49.0 4.82e-01 98.1% 88.3%
3190835 4.1.1.286 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7072 0.56 43.0 3.84e-01 96.3% 56.5%
4941620 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 46.0 4.57e-01 100.0% 91.7%
4278911 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.55 42.0 4.36e-01 88.9% 94.0%
3584364 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 41.0 4.23e-01 96.3% 96.0%
4470603 4.1.1.217 ↗ beta barrels › SH3 › SH3 › SH3 › zf-CCCH_4 0.53 43.0 3.19e-01 98.1% 33.3%
3967527 4216.1.1.1 ↗ a+b duplicates or obligate multimers › Heme iron utilization protein-like › Heme iron utilization protein-like › Heme iron utilization protein-like › HemS 0.53 41.0 3.15e-01 100.0% 47.9%