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KR052482.1__AKF13270.1__PHIN3_3__00003

Bact-Vir

KR052482.1__AKF13270.1__PHIN3_3__00003

Identity

Accession:
KR052482 ↗
Kingdom:
phage

Quality

91.2 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 medium residues 25-86
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ijjB00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.81 62.0 4.75e-01 80.6% 70.8%
4lwsA00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.80 54.0 4.61e-01 71.0% 83.0%
1a7eA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.79 68.0 5.59e-01 100.0% 64.4%
3jsbA01 1.20.1440.300 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain 0.78 66.0 5.97e-01 100.0% 69.1%
3rpmA02 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.77 68.0 6.18e-01 100.0% 76.5%
2wl8C00 1.20.120.900 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pex19, mPTS binding domain 0.76 64.0 5.35e-01 95.2% 72.5%
2qffA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.75 67.0 6.33e-01 100.0% 93.2%
2wb7A03 1.20.120.870 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › pT26-6p, five-helical bundle domain 0.74 65.0 5.08e-01 100.0% 62.5%
3zssA02 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.73 63.0 5.83e-01 98.4% 75.9%
1lq7A00 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.72 61.0 6.05e-01 98.4% 97.0%
3t46A00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.71 62.0 5.91e-01 100.0% 92.0%
1oahA02 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.71 61.0 4.75e-01 100.0% 62.0%
7p5hB03 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.68 57.0 5.11e-01 95.2% 70.8%
2c9kA01 1.20.190.10 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › Pesticidal crystal protein, N-terminal domain 0.67 57.0 3.86e-01 96.8% 41.8%
3g2fA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.67 58.0 4.01e-01 100.0% 78.4%
4jvsA01 1.20.120.1700 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.66 56.0 4.59e-01 100.0% 87.3%
6ziwI02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.65 54.0 3.96e-01 96.8% 50.5%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.64 54.0 4.50e-01 93.5% 75.0%
1rktA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.60 51.0 3.89e-01 96.8% 70.9%
1eo0A00 1.20.930.10 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.58 47.0 4.44e-01 100.0% 76.6%
2g8lB01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.57 45.0 4.47e-01 96.8% 97.0%
1musA01 1.10.246.40 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › Tn5 transposase; domain 1 0.56 45.0 4.42e-01 85.5% 84.8%
4iaoA01 1.20.120.1710 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.54 44.0 3.64e-01 98.4% 49.1%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.54 42.0 3.92e-01 95.2% 65.9%
3ilkA02 1.10.8.590 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.54 46.0 4.53e-01 100.0% 92.6%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.53 42.0 3.94e-01 96.8% 69.4%
3kdgA02 3.30.1370.100 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › MutL, C-terminal domain, regulatory subdomain 0.53 43.0 3.88e-01 95.2% 76.6%
6pmiF01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.53 42.0 3.90e-01 88.7% 85.0%
6ldiF01 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 0.52 40.0 3.59e-01 88.7% 66.7%
1rp3A01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.51 44.0 3.99e-01 98.4% 83.5%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3585459 109.4.1.2716 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CTNNBL, TFCD_C, ARM_TBCD_2nd 0.83 71.0 3.85e-01 93.5% 6.2%
3931393 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.80 70.0 5.61e-01 100.0% 58.4%
4426305 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.79 71.0 6.51e-01 100.0% 86.3%
4042010 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.78 70.0 6.56e-01 98.4% 86.7%
54604 601.14.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin 0.78 68.0 5.54e-01 100.0% 64.4%
3865887 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.78 67.0 6.10e-01 98.4% 85.9%
3589765 601.41.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › C-terminal domain in uncharacterized DUF3829-like protein › C-terminal domain in uncharacterized DUF3829-like protein 0.77 67.0 5.92e-01 96.8% 78.9%
3556027 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.77 52.0 4.71e-01 71.0% 97.6%
3855461 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.77 52.0 4.69e-01 71.0% 97.6%
3389507 3817.1.1.1 ↗ alpha bundles › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Pex19 0.76 67.0 5.43e-01 100.0% 68.3%
3902100 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.76 52.0 4.67e-01 71.0% 97.6%
3780051 3602.1.1.0 ↗ alpha bundles › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain 0.76 51.0 5.25e-01 71.0% 81.7%
2038540 3817.1.1.1 ↗ alpha bundles › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Pex19 0.75 64.0 4.93e-01 95.2% 56.8%
4034406 632.15.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › CompInhib_SCIN 0.75 66.0 5.94e-01 100.0% 83.5%
5031855 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.75 65.0 6.06e-01 100.0% 93.8%
3388565 192.8.1.372 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › KIF21A, KIF21A_4th 0.73 49.0 3.04e-01 71.0% 22.4%
3215515 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.73 62.0 5.58e-01 98.4% 86.7%
4034578 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.73 64.0 5.06e-01 100.0% 75.4%
3931994 632.15.1.10 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › IQ 0.73 62.0 5.03e-01 100.0% 67.2%
3176652 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.70 60.0 5.59e-01 100.0% 78.8%
3628391 3289.1.1.2 ↗ alpha complex topology › Nck-associated protein 1/Cytoplasmic FMR1-interacting protein 1 › Nck-associated protein 1/Cytoplasmic FMR1-interacting protein 1 › Nck-associated protein 1/Cytoplasmic FMR1-interacting protein 1 › Nckap1 0.69 58.0 3.18e-01 100.0% 6.3%
4008954 632.2.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.68 59.0 5.09e-01 100.0% 72.0%
3916497 632.8.1.17 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › Rab_eff_C 0.67 57.0 4.66e-01 98.4% 100.0%
3978162 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.67 58.0 5.01e-01 100.0% 72.0%
5060558 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.63 53.0 4.94e-01 100.0% 81.2%
3703222 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.59 47.0 4.21e-01 95.2% 67.4%
4349095 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.58 48.0 3.90e-01 90.3% 65.2%
3487862 212.1.1.0 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like 0.57 41.0 2.87e-01 80.6% 57.9%