←Back to structures

OP830907.1__WBF78131.1__MEP402_gp11__00011

Bact-Vir

OP830907.1__WBF78131.1__MEP402_gp11__00011

Identity

Accession:
OP830907 ↗
Kingdom:
phage

Quality

90.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Zobellviridae› Methylophilales_phage_MEP402

TaxID: 3003801

Cluster

View cluster (24 members)

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 7-56
PDB
Domain cluster: rep: V01127.1__CAA24348.1__X__00022__D11-55
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1nuiA01 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.83 61.0 6.57e-01 78.0% 93.0%
1vwxp00 2.20.25.30 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.77 53.0 4.28e-01 76.0% 39.6%
1jj2Y00 2.20.25.30 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.68 49.0 4.35e-01 78.0% 53.4%
2gcjA01 2.30.29.150 Mainly Beta › Roll › PH-domain like › 0.66 46.0 3.44e-01 74.0% 94.0%
2xzm901 6.20.50.180 Special › Other non-globular › N-terminal domain of TfIIb › 0.65 51.0 4.54e-01 86.0% 61.1%
2bszA01 3.30.2140.10 Alpha Beta › 2-Layer Sandwich › Arylamine N-acetyltransferase fold › Arylamine N-acetyltransferase 0.63 48.0 3.28e-01 82.0% 38.2%
3cihA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.62 45.0 3.41e-01 78.0% 41.5%
3s27B01 3.10.450.330 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.62 45.0 3.25e-01 78.0% 30.1%
2aklA01 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.61 41.0 4.28e-01 70.0% 81.4%
3x29A00 1.20.140.150 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.59 50.0 3.57e-01 100.0% 30.1%
3m7nA03 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.59 38.0 4.12e-01 74.0% 94.1%
1a6zA01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.59 49.0 3.45e-01 100.0% 54.7%
4cc9A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.58 44.0 2.73e-01 84.0% 20.8%
2oqrA03 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 0.56 39.0 3.11e-01 74.0% 79.4%
1t7vA01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.56 46.0 3.32e-01 100.0% 55.1%
1qf8A02 2.20.25.20 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.56 40.0 3.73e-01 84.0% 70.8%
4hhvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 40.0 3.35e-01 84.0% 93.2%
1kcgC00 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.54 46.0 3.25e-01 100.0% 95.3%
5cqgA04 3.30.70.2630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 38.0 3.04e-01 74.0% 78.3%
1k8iA01 3.10.320.10 Alpha Beta › Roll › Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 › Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 0.53 38.0 3.35e-01 76.0% 85.7%
3t7aA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 45.0 3.08e-01 100.0% 75.7%
4ifdI02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 37.0 2.75e-01 78.0% 26.4%
4f03A01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 33.0 2.61e-01 100.0% 29.5%
5xpyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 40.0 3.37e-01 96.0% 83.3%
5ejrA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 39.0 3.54e-01 90.0% 100.0%
6l4lA02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.52 40.0 3.09e-01 94.0% 64.7%
5a2fA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 43.0 3.44e-01 98.0% 57.5%
3lxqA01 3.30.1120.80 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.50 43.0 3.52e-01 100.0% 63.6%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5000797 375.1.1.13 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L37ae 0.77 54.0 4.70e-01 74.0% 52.0%
3790969 375.4.1.0 ↗ few secondary structure elements › Rubredoxin-like › Nucleolar RNA-binding protein Nop10-like › Nucleolar RNA-binding protein Nop10-like 0.75 50.0 5.45e-01 74.0% 87.5%
5070615 4294.1.1.0 ↗ few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like 0.72 49.0 4.98e-01 72.0% 76.0%
4943268 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.72 52.0 4.35e-01 78.0% 45.9%
1442764 375.1.1.13 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L37ae 0.71 52.0 4.09e-01 78.0% 38.2%
3709449 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.71 47.0 2.90e-01 78.0% 11.5%
5028391 375.1.1.13 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L37ae 0.70 48.0 3.92e-01 72.0% 41.9%
5042912 375.1.1.13 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L37ae 0.70 51.0 4.35e-01 78.0% 48.8%
5050229 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.69 46.0 4.11e-01 70.0% 48.6%
2642976 375.1.1.206 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L37ae, Zn_ribbon_IS1595 0.69 50.0 4.22e-01 78.0% 47.6%
4977601 375.1.1.13 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L37ae 0.68 53.0 4.44e-01 94.0% 48.9%
4928885 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.67 45.0 4.75e-01 72.0% 77.8%
4943013 375.1.1.13 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L37ae 0.67 49.0 4.01e-01 78.0% 44.4%
4932429 375.1.1.13 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_L37ae 0.66 46.0 4.32e-01 74.0% 60.3%
1530779 375.1.1.11 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Ribosomal_S27 0.65 51.0 4.12e-01 86.0% 44.9%
4929508 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.65 41.0 3.10e-01 70.0% 25.6%
4013297 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.63 54.0 3.73e-01 100.0% 33.5%
3489607 633.23.1.4 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Claudin_2 0.61 52.0 3.49e-01 100.0% 30.2%
3217200 207.1.1.52 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FBA_2 0.61 44.0 2.74e-01 78.0% 15.2%
4999913 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.61 39.0 2.99e-01 70.0% 26.4%
3514931 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.60 41.0 4.33e-01 70.0% 87.5%
5020293 375.1.1.19 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › RNA_POL_M_15KD 0.60 40.0 4.13e-01 72.0% 75.6%
3039309 2003.1.5.91 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Reovirus_L2_MT2 0.59 38.0 2.47e-01 72.0% 14.1%
3624687 64.1.1.9 ↗ beta meanders › WW domain-like › WW domain › WW domain › WW_TCERG1 0.59 38.0 3.89e-01 70.0% 68.0%
3421203 386.1.1.20 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-met 0.58 41.0 3.87e-01 74.0% 65.0%
3263070 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.57 48.0 3.22e-01 100.0% 33.0%
4437923 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.56 39.0 2.55e-01 74.0% 20.4%
4228426 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.56 40.0 3.22e-01 78.0% 80.0%
4227538 375.1.1.60 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › PriA_CRR 0.56 39.0 3.81e-01 74.0% 89.1%
4971662 2006.1.1.13 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Acid_PPase 0.54 44.0 3.14e-01 92.0% 57.5%
3562800 7512.1.1.3 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 0.51 42.0 2.83e-01 100.0% 64.3%
4160983 633.23.1.9 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 0.51 41.0 2.88e-01 100.0% 69.8%
3515928 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.51 42.0 4.23e-01 100.0% 89.8%
3553889 233.1.1.1 ↗ a+b two layers › MHC antigen-recognition domain › MHC antigen-recognition domain › MHC antigen-recognition domain › MHC_I 0.51 43.0 3.00e-01 100.0% 28.2%
5065644 2006.1.1.13 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Acid_PPase 0.50 40.0 2.82e-01 88.0% 58.3%
5025169 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 38.0 2.98e-01 92.0% 73.3%
4223286 633.23.1.9 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 0.50 41.0 2.89e-01 100.0% 33.2%
D2 medium residues 62-131
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5hr9A01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.64 37.0 3.18e-01 97.1% 36.4%
5i4eA01 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.61 37.0 4.43e-01 87.1% 93.5%
4x9cD00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.60 37.0 3.94e-01 92.9% 71.7%
4f88102 3.90.1720.60 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › 0.59 43.0 3.17e-01 80.0% 54.9%
2mysA01 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.59 34.0 4.03e-01 88.6% 85.4%
4ytlA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.58 35.0 4.06e-01 88.6% 86.0%
1nycA00 2.40.310.10 Mainly Beta › Beta Barrel › Staphostatins › beta-Barrel protease inhibitors 0.55 43.0 3.77e-01 87.1% 73.9%
4boeA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.54 43.0 3.51e-01 92.9% 89.6%
6n90A00 3.30.2310.20 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like 0.54 37.0 3.49e-01 72.9% 61.4%
6bogA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.53 33.0 3.63e-01 92.9% 82.7%
1jssA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.53 45.0 3.34e-01 100.0% 82.9%
3tfzB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.52 39.0 3.15e-01 87.1% 56.4%
4mveA00 2.40.128.580 Mainly Beta › Beta Barrel › Lipocalin › GXWXG domain 0.52 44.0 3.54e-01 97.1% 72.8%
3h6qA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.52 41.0 3.16e-01 87.1% 89.9%
3ewaA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 37.0 2.68e-01 81.4% 85.1%
1ib8A02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.51 38.0 3.89e-01 95.7% 83.6%
4hg1A00 3.40.1580.30 Alpha Beta › 3-Layer(aba) Sandwich › SMI1/KNR4-like › Domain of unknown function (DUF5066) 0.50 41.0 3.06e-01 100.0% 86.5%
1dxkA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.50 37.0 2.74e-01 82.9% 48.9%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3896126 4023.1.1.0 ↗ a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core 0.76 67.0 5.96e-01 98.6% 93.0%
5017214 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.61 36.0 3.93e-01 92.9% 72.7%
5022491 4.1.1.182 ↗ beta barrels › SH3 › SH3 › SH3 › DUF2097 0.59 42.0 3.95e-01 97.1% 61.2%
3399407 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 40.0 3.56e-01 70.0% 92.0%
4243367 3561.1.1.0 ↗ 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 0.56 40.0 2.51e-01 75.7% 26.0%
1503651 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.54 38.0 3.65e-01 88.6% 63.7%
3979396 3454.1.1.4 ↗ beta barrels › GspC HR domain/PilP-like › GspC HR domain/PilP-like › GspC HR domain/PilP-like › HofP 0.52 41.0 4.00e-01 97.1% 76.2%
3619070 331.3.1.5 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc 0.52 39.0 3.09e-01 84.3% 58.2%
1108151 9.20.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Uncharacterized protein Tcur_1030 › Uncharacterized protein Tcur_1030 › GXWXG,DUF4334 0.52 44.0 3.53e-01 97.1% 72.3%
3281799 2003.1.2.56 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › NAD_binding_9 0.51 38.0 2.34e-01 84.3% 16.0%
4946710 876.1.1.0 ↗ a+b complex topology › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParB/Sulfiredoxin 0.51 37.0 3.65e-01 82.9% 73.3%
3283509 9.4.1.0 ↗ beta barrels › Lipocalins/Streptavidin › D-aminopeptidase, middle and C-terminal domains › D-aminopeptidase, middle and C-terminal domains 0.51 44.0 3.84e-01 97.1% 76.1%
220690 4205.1.1.6 ↗ a+b two layers › SMI1/KNR4-like › SMI1/KNR4-like › SMI1/KNR4-like › DUF5066 0.50 41.0 3.06e-01 100.0% 86.5%
3591670 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.50 34.0 3.79e-01 88.6% 90.9%
D3 medium residues 132-235
PDB
Domain cluster: rep: IMGVR_UViG_3300042256_000037-3300042256-Ga0451646_00357_7329_9968__D263-392
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01751.29 best Toprim 29.4 1.00e-06 83.7% 76.0%