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LC768487.1__BEH88347.1__X__00059

Bact-Vir

LC768487.1__BEH88347.1__X__00059

Identity

Accession:
LC768487 ↗
Kingdom:
phage

Quality

82.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Alcyoneusvirus› Klebsiella_phage_phiKp_21

TaxID: 2979978

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 34-88
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.92 73.0 7.60e-01 83.6% 94.1%
4izzB02 1.10.10.1680 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › HetR, N-terminal DNA-binding domain 0.91 46.0 4.19e-01 72.7% 41.2%
2r9iA00 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.90 81.0 7.44e-01 100.0% 95.8%
4adzA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.89 81.0 6.79e-01 100.0% 65.6%
5fmnA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.89 81.0 6.89e-01 100.0% 67.4%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.88 80.0 6.78e-01 100.0% 62.8%
4wvaB00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.86 68.0 3.97e-01 92.7% 11.4%
2wmmA01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.86 63.0 6.69e-01 78.2% 95.9%
2jdiG01 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.86 77.0 7.50e-01 100.0% 96.7%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.85 75.0 7.09e-01 98.2% 82.8%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.84 74.0 6.12e-01 100.0% 59.2%
4gbjC02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.83 62.0 4.58e-01 80.0% 32.6%
1vpdA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.83 63.0 4.63e-01 80.0% 34.4%
3w5mA05 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.82 64.0 3.90e-01 87.3% 13.9%
3q18A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.82 65.0 5.08e-01 87.3% 41.4%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.81 71.0 6.18e-01 100.0% 70.6%
4dllB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.81 59.0 4.42e-01 78.2% 35.4%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.80 68.0 6.67e-01 92.7% 87.9%
5lbmA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.79 69.0 6.09e-01 100.0% 71.1%
3w6zA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.79 59.0 4.50e-01 78.2% 36.4%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.78 71.0 5.60e-01 100.0% 50.9%
5je8B02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.78 58.0 4.42e-01 80.0% 35.9%
3g0oA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.78 58.0 4.46e-01 80.0% 37.2%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 67.0 5.94e-01 100.0% 70.4%
4oe8C00 1.10.8.1170 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.78 66.0 5.64e-01 94.5% 59.8%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.75 63.0 5.73e-01 92.7% 70.3%
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.75 56.0 5.98e-01 81.8% 97.9%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.74 64.0 5.82e-01 100.0% 77.9%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 65.0 6.22e-01 100.0% 88.9%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 64.0 5.79e-01 100.0% 77.6%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.73 63.0 4.70e-01 100.0% 40.7%
1ma1A01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.73 58.0 5.61e-01 92.7% 82.8%
2dw4A03 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.73 61.0 5.14e-01 100.0% 67.3%
1egdA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.70 60.0 4.54e-01 100.0% 39.7%
3gnlB02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 51.0 4.80e-01 80.0% 66.2%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.70 52.0 5.22e-01 85.5% 84.5%
2y0eB03 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.69 61.0 4.06e-01 100.0% 73.5%
3w8hB00 1.10.12.70 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › 0.68 49.0 4.72e-01 80.0% 69.7%
5z4zC00 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 0.66 58.0 4.92e-01 98.2% 97.7%
1rsoB00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.60 43.0 4.30e-01 78.2% 78.6%
3t0yA02 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 4.31e-01 78.2% 85.0%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3934928 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.93 84.0 6.80e-01 98.2% 55.8%
4268623 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.92 76.0 5.54e-01 90.9% 36.9%
3680789 2004.1.1.505 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, AAA_30 0.91 84.0 4.88e-01 100.0% 13.4%
3932692 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.90 84.0 6.95e-01 100.0% 61.1%
4048446 148.1.3.26 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_9 0.90 83.0 5.29e-01 100.0% 29.6%
4273807 314.1.1.0 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.90 83.0 4.79e-01 100.0% 12.7%
5044642 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.89 82.0 5.16e-01 100.0% 22.0%
3940557 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.89 81.0 6.02e-01 100.0% 45.4%
3998985 4207.1.2.0 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region 0.89 81.0 6.32e-01 100.0% 50.9%
3936693 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.88 78.0 6.31e-01 100.0% 53.0%
4385365 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.88 76.0 5.88e-01 92.7% 70.0%
5025813 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.88 82.0 6.33e-01 100.0% 50.9%
3073109 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.87 80.0 7.15e-01 100.0% 79.7%
4028650 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.87 62.0 6.05e-01 74.5% 68.3%
4120406 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.87 75.0 5.84e-01 92.7% 48.2%
4110549 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.87 81.0 6.26e-01 100.0% 50.9%
4320306 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.87 80.0 6.21e-01 100.0% 50.0%
5048093 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.86 79.0 6.14e-01 100.0% 50.9%
4304756 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.86 80.0 6.18e-01 100.0% 50.9%
4231284 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.86 80.0 6.19e-01 100.0% 50.9%
3700089 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.85 75.0 7.08e-01 96.4% 83.1%
5027469 2004.1.1.29 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD 0.85 78.0 4.45e-01 100.0% 11.5%
3953703 601.33.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain › CHAD 0.85 76.0 5.63e-01 98.2% 41.4%
4057547 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.85 78.0 6.10e-01 100.0% 50.9%
3741234 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.85 78.0 6.02e-01 100.0% 48.7%
4079591 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.84 76.0 6.00e-01 100.0% 50.9%
4359654 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.84 78.0 6.06e-01 100.0% 50.9%
4429833 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.84 78.0 6.05e-01 100.0% 50.9%
4937169 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.84 77.0 5.96e-01 98.2% 50.9%
4206524 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.84 76.0 5.95e-01 100.0% 50.9%
4043484 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.84 77.0 6.03e-01 100.0% 50.9%
3314722 109.40.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › Ctf4_C 0.84 77.0 5.77e-01 100.0% 44.0%
4424778 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.84 77.0 6.02e-01 100.0% 50.9%
4175087 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.84 77.0 6.04e-01 100.0% 50.9%
4555586 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.84 76.0 6.05e-01 100.0% 53.3%
4242072 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.83 77.0 5.93e-01 100.0% 48.7%
4147453 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.83 75.0 5.91e-01 100.0% 50.9%
3497897 3939.1.1.0 ↗ alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain 0.82 76.0 6.92e-01 100.0% 80.0%
4654983 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.82 75.0 5.88e-01 100.0% 50.9%
3693465 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.82 75.0 5.72e-01 100.0% 46.7%
4335871 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.82 75.0 5.89e-01 100.0% 50.9%
3705783 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.82 74.0 6.23e-01 100.0% 64.4%
3492576 4177.1.1.5 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Vps5 0.82 72.0 4.87e-01 100.0% 62.5%
4061849 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.81 74.0 5.80e-01 100.0% 53.6%
3605626 192.12.1.0 ↗ alpha bundles › Long alpha-hairpin › Transcriptional repressor TraM › Transcriptional repressor TraM 0.81 73.0 5.86e-01 100.0% 55.2%
3839273 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.81 75.0 5.83e-01 100.0% 50.9%
2546344 3826.1.1.1 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.81 69.0 6.73e-01 94.5% 90.0%
4300676 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.81 74.0 5.77e-01 100.0% 50.9%
4470267 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.80 74.0 5.77e-01 100.0% 50.9%
4429194 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.80 73.0 5.73e-01 100.0% 50.9%
3923888 4177.1.1.5 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Vps5 0.79 68.0 4.56e-01 100.0% 27.3%
4263341 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.79 71.0 5.54e-01 100.0% 49.6%
4017151 109.4.1.1563 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_M, HAT_Syf1_CNRKL1_C, HAT_Syf1_CNRKL1_N 0.79 68.0 3.92e-01 100.0% 13.1%
4569363 109.4.1.889 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_M 0.77 67.0 4.69e-01 100.0% 30.6%
4026926 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.77 68.0 5.10e-01 100.0% 43.7%
3834594 601.27.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › MW0975(SA0943)-like › MW0975(SA0943)-like › DUF632, DUF630 0.73 61.0 4.53e-01 98.2% 51.6%
4067677 3826.1.1.25 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › GlutR_dimer 0.69 52.0 4.71e-01 100.0% 59.0%
4305639 3826.1.1.25 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › GlutR_dimer 0.62 50.0 4.55e-01 90.9% 66.7%
3653791 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.58 47.0 4.43e-01 100.0% 77.3%