←Back to structures

NC_025455.1__YP_009103148.1__S-CBP2_0040__00040

Bact-Vir

NC_025455.1__YP_009103148.1__S-CBP2_0040__00040

Identity

Accession:
NC_025455 ↗
Kingdom:
phage

Quality

54.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Autographivirales› Kembevirus› Synechococcus_phage_S-CBP2

TaxID: 756277

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 708-866
PDB
Domain cluster: rep: OP542242.1__UYB98483.1__X__00085__D34-134
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01551.30 best Peptidase_M23 37.7 2.80e-09 62.3% 64.6%
D2 medium residues 239-294
PDB
D3 medium residues 295-378
PDB
D4 medium residues 516-662
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3na7A00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.94 41.0 3.41e-01 100.0% 27.4%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.86 40.0 4.62e-01 100.0% 59.8%
2ap3A00 1.20.120.570 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YkyA-like 0.83 37.0 3.39e-01 100.0% 33.3%
3x3bA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.83 38.0 3.04e-01 100.0% 24.4%
1bf5A01 1.20.1050.20 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › STAT transcription factor, all-alpha domain 0.80 39.0 3.76e-01 100.0% 42.3%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.79 42.0 4.92e-01 100.0% 72.6%
4wpcA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.78 38.0 2.97e-01 100.0% 24.0%
5b2nA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.77 36.0 2.92e-01 100.0% 24.7%
3a8pA02 6.10.140.680 Special › Helix non-globular › Helix Hairpins › 0.74 37.0 4.23e-01 100.0% 62.3%
1l8dA00 1.10.287.510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 41.0 4.95e-01 100.0% 79.6%
2v0xA01 1.10.287.3160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 42.0 3.99e-01 100.0% 50.0%
6c1qB02 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.73 35.0 2.77e-01 99.3% 23.3%
3ddlA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.70 31.0 2.56e-01 100.0% 23.8%
1i4dA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.68 42.0 3.85e-01 100.0% 48.9%
2dw4A03 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.67 40.0 4.74e-01 100.0% 85.1%
3kdqA00 6.10.320.10 Special › Helix non-globular › Ferritin › 0.66 38.0 3.76e-01 100.0% 55.3%
3pe0A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 35.0 4.12e-01 99.3% 72.6%
2ieqA00 1.20.5.300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.64 38.0 4.92e-01 99.3% 98.9%
1x04A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.64 39.0 3.54e-01 100.0% 44.5%
1fs0G02 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.63 38.0 4.88e-01 98.6% 100.0%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.63 38.0 4.70e-01 100.0% 97.8%
2gl2B00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.62 41.0 4.65e-01 100.0% 89.9%
2e87A01 1.20.120.1190 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.61 36.0 3.57e-01 100.0% 53.8%
2efkA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.56 38.0 3.15e-01 100.0% 37.8%
7nmqA01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.55 50.0 3.82e-01 100.0% 65.7%
4cgkA01 6.10.250.3150 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.54 44.0 3.86e-01 100.0% 59.8%
2o8bB04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.53 37.0 3.93e-01 77.6% 81.7%
3aonA00 1.10.287.3240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 48.0 4.45e-01 100.0% 84.6%
4mh6A00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 40.0 3.94e-01 100.0% 75.5%
6gy8A01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.52 46.0 3.60e-01 100.0% 44.6%
3u0cA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.51 38.0 3.86e-01 98.6% 77.5%
1orjD00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.50 38.0 4.21e-01 98.6% 92.0%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3636477 4207.1.1.74 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › TPR_VPS8_2 0.88 39.0 3.18e-01 100.0% 26.7%
3797597 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.86 35.0 4.31e-01 99.3% 58.0%
3368307 3291.1.1.119 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › NET2A 0.86 41.0 5.05e-01 100.0% 70.0%
4638470 101.1.2.311 ↗ alpha arrays › HTH › HTH › winged helix domain › RNA12 0.82 41.0 3.85e-01 99.3% 42.4%
3517467 6157.1.1.0 ↗ alpha bundles › GKAP homology domain 1 › GKAP homology domain 1 › GKAP homology domain 1 0.76 33.0 3.76e-01 100.0% 51.3%
5082442 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.74 42.0 4.48e-01 100.0% 64.6%
4049927 4044.1.1.1 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Prismane 0.71 30.0 3.74e-01 98.0% 62.1%
3795092 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.71 36.0 3.80e-01 100.0% 53.3%
3206128 3567.1.1.139 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › PF29055 0.69 37.0 4.21e-01 100.0% 67.0%
3757451 3755.3.1.297 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › KIF9 0.69 44.0 4.29e-01 100.0% 59.4%
3598168 3755.1.1.0 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related 0.68 42.0 4.06e-01 100.0% 55.2%
3784176 604.1.1.132 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › KAR9 0.66 37.0 3.75e-01 98.6% 53.8%
3586523 604.12.1.45 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › PPP1R21_helical 0.63 35.0 3.28e-01 95.2% 43.4%
3367569 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.60 34.0 3.48e-01 93.9% 56.6%
3944338 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.60 44.0 4.90e-01 100.0% 94.2%
3206518 632.22.1.62 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › ATG17_like 0.59 40.0 3.55e-01 100.0% 48.1%
4125652 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.57 52.0 3.75e-01 100.0% 76.9%
3182496 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 0.57 43.0 3.22e-01 100.0% 30.9%
3730038 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.56 35.0 3.58e-01 95.9% 64.3%
3399808 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.56 38.0 3.73e-01 100.0% 64.5%
3385968 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.56 52.0 4.63e-01 100.0% 82.0%
4530382 2004.1.1.199 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23,SbcC_Walker_B 0.56 47.0 3.25e-01 92.5% 40.6%
3977409 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 0.55 41.0 4.34e-01 100.0% 83.0%
3611437 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 0.55 47.0 4.61e-01 100.0% 86.3%
3716654 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.54 38.0 3.94e-01 100.0% 77.0%
4322826 2004.1.1.525 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23, AAA_27, SbcC_Walker_B 0.54 46.0 3.15e-01 92.5% 40.6%
3730963 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.54 39.0 2.80e-01 100.0% 24.5%
5082020 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 0.54 47.0 3.65e-01 100.0% 81.4%
4026833 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.53 47.0 4.40e-01 98.0% 95.1%
5074606 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.53 35.0 4.33e-01 97.3% 100.0%
4006117 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.52 42.0 3.78e-01 100.0% 60.5%
3556456 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 46.0 3.63e-01 100.0% 68.1%
4797604 1042.1.1.1 ↗ a+b complex topology › S2 subunit of coronavirus spike glycoprotein › S2 subunit of coronavirus spike glycoprotein › S2 subunit of coronavirus spike glycoprotein › CoV_S2 0.51 36.0 4.20e-01 100.0% 99.1%
4246249 3748.1.1.3 ↗ extended segments › 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain › 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain › 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain › eIF3h_C 0.51 38.0 3.87e-01 100.0% 80.7%