←Back to structures

OP940114.1__WAX23194.1__VL10_ORF03__00003

Bact-Vir

OP940114.1__WAX23194.1__VL10_ORF03__00003

Identity

Accession:
OP940114 ↗
Kingdom:
phage

Quality

82.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Herelleviridae› Silviavirus› Staphylococcus_phage_vB_SauM_VL10

TaxID: 3003699

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 1-61
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3anwA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.90 78.0 6.19e-01 95.1% 49.6%
2hfsA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.90 68.0 4.94e-01 78.7% 32.9%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.87 64.0 6.85e-01 77.0% 90.4%
4fymF00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.86 68.0 4.55e-01 83.6% 30.1%
1cpqA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.86 70.0 5.34e-01 93.4% 41.1%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.85 61.0 5.62e-01 75.4% 60.5%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.85 64.0 5.02e-01 82.0% 41.4%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.84 60.0 6.75e-01 77.0% 100.0%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.84 73.0 5.93e-01 98.4% 51.7%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.83 72.0 5.62e-01 95.1% 80.6%
1gqeA01 1.20.58.410 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Release factor 0.82 71.0 5.71e-01 93.4% 78.8%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.80 60.0 5.63e-01 83.6% 65.3%
3kflA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.80 67.0 4.76e-01 91.8% 32.0%
1o9gA02 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.78 52.0 5.89e-01 82.0% 97.7%
3t9jA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.77 67.0 5.02e-01 96.7% 40.3%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.77 59.0 5.37e-01 83.6% 62.2%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.77 60.0 4.88e-01 85.2% 46.9%
1wleA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.77 67.0 5.45e-01 98.4% 58.8%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 67.0 6.44e-01 96.7% 85.5%
3kwoA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.76 66.0 5.00e-01 100.0% 76.5%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 66.0 6.29e-01 100.0% 90.4%
2rdcA00 1.10.287.800 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › protein ne1242 0.75 67.0 5.15e-01 98.4% 46.6%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.75 63.0 6.25e-01 91.8% 92.2%
1grjA01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.74 67.0 6.28e-01 100.0% 86.5%
7tzoA01 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.74 60.0 4.31e-01 93.4% 31.6%
3r6nA02 1.20.58.1060 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 63.0 4.79e-01 100.0% 73.5%
1j30A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.74 64.0 4.94e-01 100.0% 44.0%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 54.0 5.82e-01 82.0% 94.1%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 65.0 5.55e-01 100.0% 62.2%
1e52A00 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.72 58.0 5.98e-01 96.7% 98.2%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.69 58.0 5.72e-01 100.0% 95.6%
2x43S00 6.10.140.1430 Special › Helix non-globular › Helix Hairpins › 0.64 50.0 4.93e-01 88.5% 80.6%
2e62A01 6.10.140.420 Special › Helix non-globular › Helix Hairpins › 0.62 48.0 5.17e-01 88.5% 100.0%
3u4qA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.61 43.0 2.97e-01 77.0% 20.6%
1iuqA01 1.10.1200.50 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal 0.59 45.0 4.17e-01 90.2% 65.8%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3336677 605.1.1.132 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › DUF641 0.94 82.0 7.57e-01 91.8% 93.3%
3296414 192.29.1.168 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › DUF641 0.94 81.0 7.70e-01 91.8% 100.0%
3560750 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.90 78.0 7.38e-01 91.8% 100.0%
4618805 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.87 73.0 7.61e-01 91.8% 100.0%
3316949 4006.1.1.0 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain 0.86 78.0 5.95e-01 100.0% 45.2%
3709352 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.86 79.0 5.73e-01 100.0% 39.4%
3614617 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.85 78.0 5.79e-01 100.0% 43.4%
4859903 304.116.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in release factor › Ferredoxin-like domain in release factor › PCRF 0.85 77.0 6.07e-01 100.0% 73.1%
4212526 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.84 77.0 6.07e-01 100.0% 52.5%
3230312 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.84 69.0 6.57e-01 90.2% 77.1%
3965106 605.1.1.4 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.84 77.0 7.13e-01 100.0% 86.7%
3542527 5020.1.1.8 ↗ extended segments › Subunit VIII of photosystem I reaction centre, PsaI › Subunit VIII of photosystem I reaction centre, PsaI › Subunit VIII of photosystem I reaction centre, PsaI › TB2_DP1_HVA22 0.84 72.0 6.46e-01 98.4% 68.2%
4018440 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.83 75.0 6.44e-01 100.0% 91.6%
3513338 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.83 59.0 3.86e-01 77.0% 20.0%
3906819 192.17.1.6 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.82 74.0 5.47e-01 100.0% 42.0%
3527992 192.17.1.6 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.81 68.0 6.51e-01 93.4% 80.0%
4930709 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.81 74.0 5.07e-01 100.0% 31.3%
3753240 3291.1.1.54 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › CC2D1A-B_DM14 0.81 72.0 5.21e-01 100.0% 37.1%
4514051 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.81 72.0 5.78e-01 98.4% 54.8%
3802185 192.8.1.359 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › DUF641 0.81 72.0 6.89e-01 100.0% 90.0%
3738041 192.5.1.1 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.78 69.0 6.19e-01 98.4% 70.6%
4945931 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.77 67.0 6.37e-01 95.1% 100.0%
2750143 3758.1.1.1 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins › Bacillus_HBL 0.77 69.0 4.87e-01 100.0% 35.2%
4988301 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.76 68.0 5.10e-01 100.0% 42.0%
4960168 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.73 66.0 4.80e-01 100.0% 38.8%
3477749 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.73 66.0 6.29e-01 98.4% 88.6%
3273862 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.72 62.0 5.41e-01 100.0% 63.2%
4973347 515.1.1.4 ↗ alpha arrays › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › EMC3_TMCO1 0.71 64.0 4.61e-01 100.0% 35.9%
3167929 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.70 56.0 5.37e-01 90.2% 75.7%
4831662 5043.1.1.1 ↗ extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like › Htr2 0.70 61.0 5.95e-01 96.7% 95.5%
3213282 616.1.1.21 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › DUF4473 0.70 57.0 5.40e-01 93.4% 76.0%
5040031 632.22.1.199 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › PLDc_N 0.67 55.0 4.96e-01 93.4% 65.9%