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RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00675

Bact-Vir

RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00675

Identity

Kingdom:
phage

Quality

89.5 mean pLDDT

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 2-68
PDB
Domain cluster: representative
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4dq2A03 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.69 44.0 5.03e-01 91.0% 93.6%
7qzqA01 2.120.10.80 Mainly Beta › 6 Propeller › Neuraminidase › Kelch-type beta propeller 0.65 42.0 2.65e-01 79.1% 13.2%
3ebtA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 44.0 3.55e-01 79.1% 36.6%
3ehcB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 45.0 3.65e-01 79.1% 43.0%
3f14A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 45.0 3.80e-01 79.1% 47.3%
2k5gA01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.61 49.0 3.71e-01 92.5% 59.4%
2obdA02 3.15.10.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Bactericidal permeability-increasing protein; domain 1 0.60 53.0 3.87e-01 100.0% 66.1%
3k25A00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.60 46.0 3.03e-01 83.6% 64.9%
3gwrB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.60 44.0 3.61e-01 79.1% 43.3%
6pfzD02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.60 48.0 3.26e-01 89.6% 67.3%
3hx8A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.60 44.0 3.59e-01 79.1% 44.5%
1ukxA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.60 50.0 4.01e-01 94.0% 69.3%
3a0oA03 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.60 47.0 3.14e-01 88.1% 71.9%
2heqA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.57 41.0 4.46e-01 86.6% 94.4%
2iabA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.56 40.0 3.27e-01 79.1% 72.0%
3icsA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 44.0 3.04e-01 89.6% 38.8%
3q1nA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.56 42.0 2.84e-01 85.1% 72.4%
2pd0A01 3.30.2310.50 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › Protein of unknown function (DUF3228), domain 1 0.55 41.0 3.43e-01 79.1% 62.5%
3zo9B03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.55 40.0 3.62e-01 79.1% 91.6%
3u5wA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 38.0 3.28e-01 79.1% 80.2%
2hn1A01 3.30.460.20 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like 0.52 38.0 2.97e-01 83.6% 35.9%
3ktaA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 44.0 3.41e-01 98.5% 81.1%
2htaA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.52 40.0 2.74e-01 89.6% 22.6%
3kglB01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.50 44.0 3.11e-01 100.0% 57.0%
3bpnC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 45.0 3.95e-01 100.0% 95.0%
3hufA01 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.50 41.0 3.60e-01 98.5% 94.8%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3278140 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.71 47.0 3.94e-01 79.1% 40.9%
3933168 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.68 57.0 4.12e-01 91.0% 35.6%
4011818 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.67 59.0 3.79e-01 98.5% 34.5%
5021621 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.63 47.0 3.75e-01 79.1% 81.5%
4023469 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.63 53.0 4.21e-01 94.0% 66.4%
3618875 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.61 50.0 4.10e-01 95.5% 70.4%
5048901 247.1.1.1 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B 0.59 45.0 3.05e-01 100.0% 20.7%
1770212 244.2.1.1 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Pyr_redox_dim 0.57 45.0 3.75e-01 89.6% 80.0%
3247995 4.1.1.33 ↗ beta barrels › SH3 › SH3 › SH3 › Myosin_N 0.57 39.0 3.89e-01 88.1% 65.7%
3931298 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.56 47.0 3.87e-01 95.5% 67.2%
2485465 1.1.5.31 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyridox_ox_2 0.55 39.0 2.91e-01 79.1% 57.5%
3991810 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.55 46.0 3.61e-01 95.5% 60.7%
3280271 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.55 49.0 4.11e-01 100.0% 73.0%
3386801 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.54 48.0 4.21e-01 98.5% 66.0%
1878579 244.2.1.1 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Pyr_redox_dim 0.54 42.0 3.51e-01 89.6% 79.2%
3952896 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.53 42.0 3.56e-01 91.0% 82.3%
4982246 3521.1.1.0 ↗ a+b three layers › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain 0.53 46.0 4.08e-01 100.0% 77.0%
3574882 227.1.1.12 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.53 36.0 2.88e-01 70.1% 52.2%
4872018 10.12.1.3 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_1 0.53 41.0 3.63e-01 85.1% 57.6%
4971321 244.2.1.1 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Pyr_redox_dim 0.53 40.0 3.41e-01 89.6% 76.9%
1309072 10.12.1.3 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_1 0.52 41.0 3.92e-01 85.1% 74.0%
3704394 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.52 44.0 2.98e-01 97.0% 54.5%
4023315 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.52 43.0 3.91e-01 92.5% 77.8%
5060374 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.51 44.0 2.79e-01 98.5% 39.5%
3694872 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.51 40.0 2.57e-01 92.5% 25.1%
3487683 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 42.0 2.53e-01 92.5% 20.0%