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MK016498.1__AYQ99814.1__PBI_MANDA_138__00136

Bact-Vir

MK016498.1__AYQ99814.1__PBI_MANDA_138__00136

Identity

Accession:
MK016498 ↗
Kingdom:
phage

Quality

54.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Kostyavirus› Mycobacterium_phage_Manda

TaxID: 2484211

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 6-106
PDB
D2 high residues 151-203
PDB
Domain cluster: representative
CATH (56)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1hqz800 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.75 55.0 4.13e-01 88.7% 31.8%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.71 59.0 4.30e-01 100.0% 55.7%
5d1oA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.71 57.0 5.19e-01 100.0% 65.8%
7wq5A01 3.30.730.10 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain 0.69 48.0 4.75e-01 75.5% 69.0%
4lizA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.69 52.0 3.86e-01 88.7% 31.9%
1j5yA02 3.30.1340.20 Alpha Beta › 2-Layer Sandwich › Histidine-containing Protein; Chain: A; › 3H domain 0.68 49.0 3.98e-01 79.2% 97.2%
3zoqC00 6.20.250.30 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.68 52.0 5.29e-01 92.5% 88.7%
3egrA00 3.10.20.520 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phenylacetic acid degradation B 0.68 55.0 5.27e-01 94.3% 84.1%
2qz8A02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.67 52.0 4.61e-01 88.7% 91.4%
3hluA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 53.0 4.83e-01 94.3% 100.0%
5z06B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 52.0 4.41e-01 100.0% 54.3%
2pttB00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 55.0 4.41e-01 100.0% 63.9%
4d7pA00 2.60.40.730 Mainly Beta › Sandwich › Immunoglobulin-like › SOR catalytic domain 0.63 53.0 4.48e-01 100.0% 84.4%
1pgsA01 2.60.120.230 Mainly Beta › Sandwich › Jelly Rolls › 0.63 53.0 4.07e-01 100.0% 74.1%
1wfuA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 54.0 4.56e-01 100.0% 60.0%
3mpcA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 53.0 4.35e-01 100.0% 52.1%
4ccjA01 2.60.120.650 Mainly Beta › Sandwich › Jelly Rolls › Cupin 0.63 52.0 3.45e-01 100.0% 21.5%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.63 47.0 3.56e-01 88.7% 33.6%
2crfA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 51.0 3.98e-01 96.2% 74.4%
1wgrA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.62 53.0 4.67e-01 100.0% 80.5%
5yjlD01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.62 53.0 3.95e-01 100.0% 38.0%
2h6uA00 2.60.40.180 Mainly Beta › Sandwich › Immunoglobulin-like › Transthyretin/hydroxyisourate hydrolase domain 0.61 51.0 4.10e-01 100.0% 52.6%
2aq6A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 51.0 3.84e-01 100.0% 42.7%
2xqxA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.61 51.0 3.81e-01 100.0% 59.2%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.60 45.0 3.91e-01 86.8% 55.4%
1cfyA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.60 44.0 3.42e-01 86.8% 33.1%
3au4A02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.60 49.0 4.22e-01 100.0% 77.7%
2j1aA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.59 49.0 3.72e-01 100.0% 63.1%
2kvkA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.59 46.0 3.42e-01 88.7% 31.9%
2e1qC01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.58 49.0 4.20e-01 100.0% 64.1%
4ekuA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.58 48.0 3.85e-01 100.0% 62.4%
4yhbA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.58 47.0 3.72e-01 100.0% 66.7%
2h6cA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.57 48.0 3.73e-01 100.0% 49.6%
4kncA02 2.60.120.1380 Mainly Beta › Sandwich › Jelly Rolls › C-terminal carbohydrate-binding module 0.57 47.0 3.79e-01 100.0% 75.2%
1qfoC00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 48.0 3.85e-01 100.0% 81.6%
5eliA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 46.0 3.80e-01 100.0% 67.9%
1s55A00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.56 46.0 3.45e-01 100.0% 71.8%
2crmA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 47.0 4.22e-01 100.0% 69.6%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 45.0 3.89e-01 100.0% 75.5%
2jjuA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 47.0 3.86e-01 100.0% 78.1%
3am2A02 2.60.120.1050 Mainly Beta › Sandwich › Jelly Rolls › 0.55 47.0 3.71e-01 100.0% 63.2%
3tcaA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.55 45.0 3.94e-01 100.0% 73.3%
3kq4B02 2.60.120.290 Mainly Beta › Sandwich › Jelly Rolls › Spermadhesin, CUB domain 0.54 44.0 3.59e-01 100.0% 90.7%
2m2dA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 45.0 3.62e-01 100.0% 78.8%
1gwmA00 2.60.120.430 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding lectin 0.54 44.0 3.33e-01 100.0% 52.3%
2qcsB02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.54 46.0 3.59e-01 100.0% 54.4%
2e26A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 43.0 3.30e-01 100.0% 95.5%
3shrA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.53 45.0 3.41e-01 100.0% 49.6%
1wkyA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 43.0 3.31e-01 100.0% 60.4%
3dn7A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 44.0 3.33e-01 100.0% 47.6%
1o5lA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 44.0 3.40e-01 100.0% 52.7%
2pqqA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 42.0 3.23e-01 100.0% 46.3%
2g5dA01 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.52 41.0 3.01e-01 100.0% 84.6%
4ev0D01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.51 41.0 3.24e-01 100.0% 49.6%
3c9aA02 2.20.20.150 Mainly Beta › Single Sheet › Anthopleurin-A › 0.51 39.0 3.81e-01 90.6% 88.5%
1a8mA00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.50 42.0 3.14e-01 100.0% 86.2%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3587109 304.5.1.7 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.73 57.0 4.82e-01 86.8% 81.1%
3665387 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.71 54.0 4.33e-01 86.8% 41.9%
3484685 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.70 51.0 3.91e-01 88.7% 32.3%
3667379 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.70 52.0 3.89e-01 88.7% 32.3%
4975793 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.70 51.0 3.85e-01 86.8% 32.3%
3455210 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.70 53.0 3.86e-01 86.8% 30.3%
146929 3115.3.1.1 ↗ a+b two layers › GP2-like › P56 › P56 › UDG-inhib_P56 0.68 52.0 5.16e-01 88.7% 82.1%
3813458 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.65 50.0 5.15e-01 86.8% 96.0%
3216548 10.12.1.40 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › JmjC_2 0.63 53.0 3.24e-01 100.0% 14.9%
3958897 4187.2.1.0 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.63 53.0 4.20e-01 100.0% 51.7%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.63 47.0 4.76e-01 86.8% 94.0%
1106820 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.63 47.0 3.56e-01 88.7% 33.6%
4028489 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.62 48.0 3.70e-01 86.8% 39.2%
3939821 10.12.1.40 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › JmjC_2 0.62 52.0 3.19e-01 100.0% 15.2%
4554731 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.62 48.0 3.26e-01 100.0% 20.9%
1692156 10.12.1.40 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › JmjC_2 0.62 52.0 3.22e-01 100.0% 16.0%
3575366 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.62 52.0 4.41e-01 100.0% 73.7%
4177440 10.12.1.40 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › JmjC_2 0.62 51.0 3.17e-01 100.0% 15.2%
3929801 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.62 52.0 4.39e-01 100.0% 78.9%
3389065 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.61 50.0 4.12e-01 100.0% 63.6%
5080205 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.61 47.0 4.87e-01 94.3% 94.0%
3942988 4187.2.1.1 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 › NAGPA 0.61 50.0 4.82e-01 100.0% 100.0%
3472961 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.60 40.0 3.03e-01 75.5% 25.3%
4941843 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.60 50.0 3.84e-01 100.0% 93.3%
3594262 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.60 50.0 3.77e-01 100.0% 49.0%
3520074 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.59 49.0 4.27e-01 100.0% 78.9%
3842874 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.59 48.0 4.03e-01 100.0% 73.3%
3925291 220.1.1.4 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Ran_BP1 0.59 48.0 3.79e-01 98.1% 70.0%
3551231 221.1.1.87 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › FERM_N_2 0.59 49.0 4.08e-01 100.0% 65.7%
5047755 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.59 44.0 3.42e-01 88.7% 33.6%
4977919 329.1.1.2 ↗ a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › DUF4443 0.58 39.0 3.21e-01 73.6% 36.2%
5009283 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 50.0 3.97e-01 100.0% 87.0%
3470213 11.1.1.223 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ceramidse_alk_C 0.58 49.0 3.68e-01 100.0% 70.7%
3940885 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.57 46.0 3.92e-01 100.0% 73.0%
3326623 221.1.1.166 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PF26130 0.56 47.0 4.39e-01 100.0% 78.6%
3935404 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.56 45.0 4.01e-01 100.0% 81.1%
3938488 10.2.1.0 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.56 46.0 3.26e-01 100.0% 33.3%
3401129 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.56 46.0 3.11e-01 100.0% 32.8%
3535416 10.4.1.0 ↗ beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain 0.56 46.0 3.48e-01 100.0% 88.3%
3401548 221.1.1.69 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › SNX17-27-31_F1_FERM 0.55 45.0 3.83e-01 100.0% 69.0%
3618720 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.55 45.0 3.87e-01 100.0% 75.8%
3582714 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.55 45.0 3.86e-01 100.0% 75.8%
3700526 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 47.0 3.78e-01 100.0% 72.7%
3455769 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.55 44.0 3.55e-01 100.0% 44.5%
3990833 382.1.1.13 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › Ly-6_related 0.55 43.0 3.73e-01 94.3% 83.2%
3398883 10.32.1.28 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Sad1_UNC 0.55 45.0 3.29e-01 100.0% 52.0%
4989530 223.1.1.23 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.55 48.0 3.42e-01 98.1% 69.0%
3620456 221.1.1.64 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Formin_GBD_N 0.55 46.0 3.76e-01 100.0% 57.3%
3644383 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.54 46.0 3.80e-01 100.0% 77.0%
3849943 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.53 39.0 3.00e-01 84.9% 57.2%
3931349 220.1.1.2 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › WH1 0.53 42.0 3.23e-01 92.5% 79.1%
3248345 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.53 40.0 3.16e-01 88.7% 35.6%
3825952 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.53 44.0 3.65e-01 100.0% 88.6%
1174 10.32.1.70 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Mann_GBD_bact 0.53 43.0 3.31e-01 100.0% 60.4%
3855388 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.52 39.0 3.37e-01 86.8% 86.3%
3915527 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.52 42.0 3.78e-01 100.0% 65.3%
3706447 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.51 39.0 3.22e-01 94.3% 79.2%
3467156 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.50 39.0 3.26e-01 94.3% 66.4%