Back to structures

rifcsphigho2-12_scaffold_combined_curated_prodigal-single.1__X__X__00138

Bact-Vir

rifcsphigho2-12_scaffold_combined_curated_prodigal-single.1__X__X__00138

Identity

Kingdom:
phage

Quality

74.7 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 3-72
PDB
Domain cluster: representative
CATH (51)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4o9gA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.70 39.0 3.04e-01 90.0% 27.5%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.69 45.0 4.64e-01 90.0% 71.2%
1b04A02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.67 46.0 4.13e-01 90.0% 50.5%
1dgsA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.65 45.0 4.08e-01 90.0% 52.6%
7l6yA01 2.40.100.10 Mainly Beta › Beta Barrel › Cyclophilin › Cyclophilin-like 0.65 58.0 4.16e-01 100.0% 98.1%
2bnmA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.65 36.0 3.03e-01 90.0% 30.8%
2edyA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 40.0 3.55e-01 90.0% 41.7%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.63 44.0 3.38e-01 87.1% 31.1%
2v5yA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 42.0 3.75e-01 91.4% 49.0%
3ir9A02 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.62 42.0 3.54e-01 92.9% 41.7%
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.61 47.0 4.34e-01 88.6% 65.2%
1fyhB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 42.0 3.73e-01 90.0% 49.5%
3cp3A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 44.0 3.58e-01 90.0% 41.7%
2hq9B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 42.0 3.39e-01 90.0% 37.2%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.61 43.0 3.92e-01 87.1% 56.5%
3u5wA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 42.0 3.46e-01 90.0% 40.5%
1va0B02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.60 35.0 2.94e-01 90.0% 32.3%
5irbA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 41.0 3.57e-01 90.0% 46.2%
3ec6A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 42.0 3.45e-01 90.0% 40.6%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.59 42.0 3.84e-01 92.9% 56.4%
2a2jA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 43.0 3.11e-01 92.9% 27.1%
4ikbA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.58 44.0 3.67e-01 82.9% 77.5%
4yo1A01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.58 43.0 3.98e-01 98.6% 61.8%
2npnA02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.57 38.0 3.37e-01 90.0% 45.0%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.57 38.0 3.76e-01 91.4% 64.5%
2r7kA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.57 38.0 4.02e-01 91.4% 78.7%
2iq1A00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.57 42.0 2.93e-01 81.4% 35.8%
4oxwA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.57 42.0 3.76e-01 82.9% 84.9%
3p0cA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.55 41.0 3.59e-01 81.4% 79.3%
2ed8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 34.0 3.30e-01 92.9% 50.0%
5cvmA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.54 47.0 3.13e-01 100.0% 31.2%
5f7uA06 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 39.0 3.23e-01 90.0% 42.1%
8bs9A01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.54 47.0 3.15e-01 100.0% 34.0%
1ywlA00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.54 38.0 3.50e-01 90.0% 55.2%
1xdnA02 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.54 38.0 3.00e-01 75.7% 80.6%
3cp7A01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 38.0 3.39e-01 92.9% 49.5%
1yqsA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 43.0 2.78e-01 90.0% 81.2%
7rtyA01 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.53 38.0 2.64e-01 75.7% 35.3%
4l63A00 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.53 38.0 2.63e-01 75.7% 59.8%
2pn5A01 2.60.40.2950 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 36.0 3.28e-01 90.0% 52.7%
5f1mA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.53 38.0 2.70e-01 78.6% 38.2%
2q0oA01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.53 37.0 2.89e-01 74.3% 55.4%
4xhyA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 41.0 3.21e-01 100.0% 37.3%
1lfwA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 41.0 3.66e-01 87.1% 100.0%
5jpnB04 2.60.120.1540 Mainly Beta › Sandwich › Jelly Rolls › 0.52 35.0 2.97e-01 90.0% 40.5%
3q8pB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.52 42.0 3.66e-01 90.0% 59.3%
1w99A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 42.0 3.07e-01 90.0% 35.1%
3zq5A03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.51 36.0 2.92e-01 77.1% 45.1%
4jndA02 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.51 40.0 2.83e-01 94.3% 61.9%
2pw9C03 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.51 41.0 3.40e-01 94.3% 52.2%
1r9fA01 3.30.390.180 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › RNA silencing suppressor P19 0.50 42.0 3.76e-01 100.0% 70.6%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4448678 4.1.1.307 beta barrels › SH3 › SH3 › SH3 › PF26132 0.84 68.0 6.68e-01 87.1% 97.3%
5007504 4121.1.1.1 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.72 44.0 2.96e-01 92.9% 16.2%
5059354 2492.1.1.61 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › MOFRL 0.71 60.0 4.93e-01 94.3% 56.9%
5017559 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.70 55.0 5.67e-01 85.7% 100.0%
4943252 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.70 53.0 4.13e-01 98.6% 38.6%
185296 862.1.1.4 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › RepB_primase 0.69 45.0 3.25e-01 90.0% 23.6%
4979507 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.69 51.0 3.96e-01 98.6% 36.9%
3188268 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.68 42.0 2.72e-01 90.0% 13.7%
3723602 4121.1.1.1 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.67 42.0 2.71e-01 90.0% 13.1%
3724523 4121.1.1.7 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › PF26616 0.67 54.0 3.43e-01 97.1% 17.5%
4397568 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.67 46.0 4.28e-01 95.7% 56.7%
3693314 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.66 41.0 2.64e-01 91.4% 12.8%
5081134 3986.2.1.0 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.66 45.0 4.81e-01 97.1% 83.3%
4959407 304.163.1.3 a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain › PF31118 0.66 42.0 4.78e-01 92.9% 90.0%
3970696 821.1.1.0 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.65 41.0 3.54e-01 100.0% 39.8%
4448433 75.1.1.1 beta barrels › Cyclophilin-like › Cyclophilin-like › Cyclophilin-like › Pro_isomerase 0.65 58.0 4.15e-01 100.0% 82.4%
4655745 264.2.1.0 beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.64 52.0 4.59e-01 87.1% 96.0%
3972526 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.63 52.0 5.23e-01 92.9% 95.7%
3467170 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.63 45.0 4.69e-01 90.0% 85.7%
5049794 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.62 54.0 4.21e-01 94.3% 51.0%
3488754 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 50.0 4.05e-01 90.0% 57.8%
3362224 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.61 42.0 4.21e-01 90.0% 68.9%
3890802 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 41.0 3.76e-01 90.0% 52.6%
3849251 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 38.0 3.49e-01 90.0% 47.4%
4990154 264.2.1.0 beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.59 47.0 4.10e-01 88.6% 98.2%
4228966 264.2.1.0 beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.59 48.0 4.19e-01 91.4% 96.4%
3696767 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.58 46.0 2.87e-01 90.0% 15.0%
4151900 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.58 52.0 4.11e-01 100.0% 50.7%
3637444 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.58 40.0 2.80e-01 90.0% 20.4%
3363261 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.57 43.0 3.60e-01 97.1% 43.7%
4847420 5089.1.1.1 beta complex topology › Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains › Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains › Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains › Thiol_cytolysin 0.57 42.0 2.98e-01 82.9% 52.0%
3612075 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.57 35.0 2.53e-01 90.0% 20.0%
5002457 1.1.5.8 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.57 44.0 3.66e-01 90.0% 48.0%
4418351 264.2.1.0 beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.56 48.0 4.21e-01 97.1% 96.2%
4272488 1.1.1.7 beta barrels › cradle loop barrel › RIFT-related › acid protease › tRNA-synt_1_2 0.55 47.0 3.45e-01 97.1% 96.5%
3951474 1.1.5.9 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx,PNP_phzG_C 0.55 43.0 3.08e-01 97.1% 28.0%
3213931 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.54 44.0 3.60e-01 90.0% 50.0%
4271892 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.54 44.0 3.64e-01 90.0% 52.0%
3937491 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 41.0 3.28e-01 90.0% 42.2%
3820431 210.2.1.1 a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.54 43.0 2.82e-01 92.9% 91.2%
5065792 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.53 47.0 3.68e-01 100.0% 47.1%
3482807 277.1.1.0 a+b two layers › PX domain › PX domain › PX domain 0.53 42.0 3.71e-01 87.1% 98.1%
3715519 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 39.0 2.87e-01 78.6% 33.7%
5045308 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.53 38.0 2.91e-01 77.1% 51.7%
3941016 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.53 47.0 3.73e-01 95.7% 54.8%
4935672 2492.1.1.7 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.53 44.0 3.54e-01 94.3% 53.6%
5027350 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.52 46.0 3.69e-01 98.6% 62.3%
5067811 219.1.1.13 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core 0.52 46.0 3.38e-01 100.0% 79.5%
4946228 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.52 36.0 2.98e-01 72.9% 76.9%
3938183 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.52 47.0 4.08e-01 100.0% 91.4%
4954188 2492.1.1.7 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.52 44.0 3.46e-01 94.3% 50.3%
3366484 210.2.1.1 a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.51 37.0 2.55e-01 80.0% 77.2%
5020151 2492.1.1.7 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.51 42.0 3.45e-01 94.3% 57.0%
5047755 2492.1.1.7 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.51 42.0 3.43e-01 95.7% 55.7%
4024700 2484.1.1.2 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.50 44.0 2.76e-01 100.0% 17.8%
4024428 4121.1.1.2 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.50 42.0 2.80e-01 92.9% 32.3%