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KR052482.1__AKF13640.1__PHIN3_377__00377

Bact-Vir

KR052482.1__AKF13640.1__PHIN3_377__00377

Identity

Accession:
KR052482 ↗
Kingdom:
phage

Quality

64.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiN3

TaxID: 1647405

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 4-66
PDB
Domain cluster: rep: H2c1_full_idba_ud_scaffold_88_prodigal-single.1__X__X__00302__D5-65
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.64 58.0 4.22e-01 100.0% 40.1%
2mngA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.64 45.0 3.59e-01 100.0% 35.9%
2bbhA01 3.30.460.20 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like 0.64 50.0 3.74e-01 100.0% 35.1%
7ejoB01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.64 56.0 5.17e-01 100.0% 98.8%
6b9tF01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.62 45.0 3.62e-01 100.0% 39.2%
1g6gB00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.62 49.0 4.01e-01 88.9% 94.4%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.62 44.0 3.78e-01 88.9% 48.0%
3bcwA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.61 39.0 3.41e-01 100.0% 40.4%
2f4pA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.60 40.0 3.19e-01 100.0% 32.8%
1u3eM02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.60 44.0 4.39e-01 87.3% 76.5%
2d93A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 42.0 3.35e-01 100.0% 35.8%
2yn5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 42.0 3.95e-01 92.1% 60.8%
1o5uA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 38.0 3.46e-01 100.0% 46.6%
3vzbB02 2.60.200.40 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.59 48.0 3.37e-01 88.9% 96.9%
4hltA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 40.0 2.97e-01 100.0% 27.6%
3l5iA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 43.0 3.84e-01 92.1% 58.0%
4m0wA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.56 50.0 3.88e-01 100.0% 46.0%
1ywlA00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.56 41.0 3.65e-01 87.3% 53.1%
3loiA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 42.0 3.18e-01 100.0% 32.5%
2pwyA01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.56 43.0 4.42e-01 85.7% 98.2%
1tq5A02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.55 38.0 3.15e-01 100.0% 37.6%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.55 44.0 3.86e-01 88.9% 60.4%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.55 44.0 3.59e-01 88.9% 56.3%
2vecA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.54 38.0 3.18e-01 100.0% 38.7%
1o54A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.54 42.0 4.04e-01 85.7% 79.2%
4ggmX02 3.40.140.80 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › LpxI C-terminal catalytic domain 0.53 45.0 3.51e-01 100.0% 44.7%
1yudA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.53 40.0 3.05e-01 100.0% 34.2%
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.52 32.0 3.32e-01 85.7% 64.9%
1i9gA01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.52 40.0 4.06e-01 85.7% 89.1%
5eh1A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 41.0 3.59e-01 90.5% 56.8%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.52 47.0 3.60e-01 100.0% 46.7%
3f6zB01 2.40.128.200 Mainly Beta › Beta Barrel › Lipocalin › C-type lysozyme inhibitor 0.51 38.0 3.63e-01 84.1% 94.9%
2kgfA00 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.51 41.0 3.27e-01 93.7% 93.6%
3gldA02 2.60.40.1140 Mainly Beta › Sandwich › Immunoglobulin-like › Collagen-binding surface protein Cna, B-type domain 0.51 44.0 3.50e-01 100.0% 81.6%
5hdwA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.51 38.0 3.17e-01 87.3% 97.7%
6tuaA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.50 39.0 2.88e-01 88.9% 74.3%
4e9jA02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.50 36.0 3.58e-01 77.8% 95.7%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3624293 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.73 55.0 4.73e-01 87.3% 52.6%
3931629 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.67 51.0 4.50e-01 87.3% 54.7%
3958896 4187.2.1.0 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.67 46.0 4.69e-01 85.7% 75.0%
3705856 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.63 53.0 3.42e-01 100.0% 20.0%
4949745 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.63 49.0 3.20e-01 100.0% 20.4%
3883408 304.151.1.2 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain of receptor-type protein tyrosine phosphatase › Ferredoxin-like domain of receptor-type protein tyrosine phosphatase › EPCAM-Trop-2_C 0.63 51.0 4.07e-01 88.9% 88.8%
3438320 304.3.1.1 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.61 36.0 3.46e-01 74.6% 48.0%
3315163 3125.1.1.1 ↗ alpha arrays › Asl3597 › Asl3597 › Asl3597 › CRR7 0.61 49.0 4.63e-01 88.9% 96.0%
5006901 10.12.1.39 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_2 0.60 40.0 3.42e-01 100.0% 40.0%
3400250 379.1.1.3 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors › Kazal_2 0.60 35.0 3.78e-01 87.3% 70.0%
3721580 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.60 49.0 3.20e-01 100.0% 20.4%
3561689 223.1.1.71 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › VGCC_alpha2 0.59 49.0 3.20e-01 90.5% 42.4%
3508377 304.9.1.79 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › PF28976 0.59 46.0 3.77e-01 87.3% 65.0%
4016056 10.12.1.39 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_2 0.58 38.0 2.90e-01 100.0% 26.1%
3617960 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.58 46.0 3.60e-01 87.3% 61.5%
3734369 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.57 50.0 3.22e-01 100.0% 23.9%
3621342 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.57 47.0 4.05e-01 88.9% 77.9%
4954535 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.57 38.0 3.30e-01 82.5% 45.3%
3704667 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.57 50.0 3.17e-01 100.0% 21.5%
3690519 3561.1.1.1 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 17 › Mediator of RNA polymerase II transcription subunit 17 › Mediator of RNA polymerase II transcription subunit 17 › Med17 0.56 49.0 2.96e-01 98.4% 31.0%
3942510 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.56 41.0 3.63e-01 88.9% 52.6%
3970207 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.56 38.0 3.30e-01 100.0% 43.8%
4955531 2002.1.1.30 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.56 47.0 3.07e-01 96.8% 26.5%
3618240 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.55 45.0 3.86e-01 88.9% 73.0%
4397568 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.55 40.0 3.60e-01 88.9% 55.6%
4158495 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.55 40.0 3.61e-01 88.9% 55.6%
4995409 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.55 41.0 2.86e-01 85.7% 44.8%
3172411 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.54 43.0 3.85e-01 87.3% 82.2%
3603549 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 44.0 4.11e-01 88.9% 74.4%
3590658 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 44.0 4.27e-01 88.9% 92.9%
3630069 223.1.1.101 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PF30734 0.54 46.0 2.64e-01 93.7% 29.0%
5017559 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 42.0 4.22e-01 85.7% 98.5%
3987692 822.3.1.1 ↗ a+b two layers › GYF/BRK domain-like › conserved domain protein SP_1775 › conserved domain protein SP_1775 › DUF4649 0.54 46.0 4.54e-01 100.0% 90.0%
4623707 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.53 39.0 3.44e-01 88.9% 52.6%
3250477 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 47.0 3.83e-01 100.0% 73.1%
3211117 304.112.1.0 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.53 42.0 3.52e-01 88.9% 87.0%
153859 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.52 32.0 3.32e-01 85.7% 64.9%
3284966 206.1.1.70 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, ABC1 0.52 42.0 2.77e-01 92.1% 49.3%
5007278 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.52 44.0 3.44e-01 92.1% 66.2%
3696767 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.52 45.0 2.79e-01 100.0% 17.5%
3255528 511.1.1.0 ↗ beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.52 46.0 3.54e-01 100.0% 58.6%
4937645 11.1.1.103 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CARDB 0.52 39.0 3.59e-01 87.3% 63.7%
3880552 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 45.0 3.19e-01 100.0% 68.2%
2126757 170.2.1.1 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24 0.51 41.0 3.27e-01 93.7% 93.6%
168756 2003.1.1.48 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › YjeF_N 0.51 38.0 2.65e-01 90.5% 22.9%
1096061 3375.1.1.1 ↗ beta barrels › Single-stranded DNA-binding protein DdrB › Single-stranded DNA-binding protein DdrB › Single-stranded DNA-binding protein DdrB › DdrB 0.51 42.0 3.48e-01 100.0% 95.3%
3606454 4357.1.1.0 ↗ beta barrels › WWE domain › WWE domain › WWE domain 0.50 38.0 3.82e-01 87.3% 98.5%
3200355 72.1.1.0 ↗ beta sandwiches › gamma-Crystallin-like › gamma-Crystallin-like › gamma-Crystallin-like 0.50 43.0 3.91e-01 100.0% 100.0%
D2 high residues 77-151
PDB