SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "C7D0R3-MurB-E-faecalis" submitted to SWISS-MODEL workspace on Oct. 17, 2017, 3:34 p.m..The submitted primary amino acid sequence is given in Table T1.

If you use any results in your research, please cite the relevant publications:

Marco Biasini; Stefan Bienert; Andrew Waterhouse; Konstantin Arnold; Gabriel Studer; Tobias Schmidt; Florian Kiefer; Tiziano Gallo Cassarino; Martino Bertoni; Lorenza Bordoli; Torsten Schwede. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research (1 July 2014) 42 (W1): W252-W258; doi: 10.1093/nar/gku340.
Arnold, K., Bordoli, L., Kopp, J. and Schwede, T. (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 22, 195-201.
Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350

Results

The SWISS-MODEL template library (SMTL version 2017-10-11, PDB release 2017-10-06) was searched with Blast (Altschul et al., 1997) and HHBlits (Remmert, et al., 2011) for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 153 templates were found (Table T2).

Models

The following models were built (see Materials and Methods "Model Building"):

Model #01

FileBuilt withOligo-StateLigandsGMQEQMEAN
PDB ProMod3 Version 1.0.2. MONOMER
None
0.78-0.77
QMEAN-0.77
0.13
All Atom-0.75
Solvation-0.10
Torsion-0.77
TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
3tx1.1.A57.84monomerBLASTX-ray2.69Å0.46 13 - 299 0.96UDP-N-acetylenolpyruvoylglucosamine reductase
LigandAdded to ModelDescription
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
GOL✕ - Not biologically relevant.
GLYCEROL
GOL✕ - Not biologically relevant.
GLYCEROL
SO4✕ - Not biologically relevant.
SULFATE ION
SO4✕ - Not biologically relevant.
SULFATE ION

Target    MNTKAMLETLNEITLLVDEPLKNVTFTKTGGPADVLALPKTKKEVEEIVAYCREQGLSWLVLGNASNLIVRDGGIRDVVI
3tx1.1.A ------------IAIKLNEPLSKYTYTKTGGAADVFVMPKTIEEAQEVVAYCHQNKIPLTILGNGSNLIIKDGGIRGVIL

Target MLTEMKEIKVAGTTMIVDAGAKLIDTTYEALAADLTGFEFACGIPGSVGGAVYMNAGAYGGEIKDVFQSAEVLLADGTIQ
3tx1.1.A HLDLLQTIERNNTQIVAMSGAKLIDTAKFALNESLSGLEFACGIPGSIGGALHMNAGAYGGEISDVLEAATVLTQTGELK

Target TMTKEDLNFRYRHSEIQELHCIVLQATFALEKGNHAEIKAQMDELTELRELKQPLEYPSCGSVFKRPVGHFTGKLIQDAG
3tx1.1.A KLKRSELKAAYRFSTIAEKNYIVLDATFSLALEEKNLIQAKMDELTAAREAKQPLEYPSCGSVFKRPPGHFAGKLIQDSG

Target LQGLKWGGAQISEKHAGFIVNIDHATATDYVELIAHIQEVIKEKFDVELQTEVRIIGEEV
3tx1.1.A LQGHIIGGAQVSLKHAGFIVNIGGATATDYMNLIAYVQQTVREKFDVELETEVKIIGED-




Model #02

FileBuilt withOligo-StateLigandsGMQEQMEAN
PDB ProMod3 Version 1.0.2. MONOMER (matching prediction)
None
0.49-5.32
QMEAN-5.32
-2.66
All Atom-3.11
Solvation-1.46
Torsion-4.70
TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
1w1l.1.A15.87homo-dimerHHblitsX-ray2.70Å0.26 4 - 287 0.90VANILLYL-ALCOHOL OXIDASE
LigandAdded to ModelDescription
EUG✕ - Binding site not conserved.
2-METHOXY-4-VINYL-PHENOL
EUG✕ - Binding site not conserved.
2-METHOXY-4-VINYL-PHENOL
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE

Target    MNTKAMLETLNEITLL--------VDE-PLKNVTFT-------KTGGPADVLALPKTKKEVEEIVAYCREQGLSWLVLGN
1w1l.1.A ---QDIIRIVGSENVEVISSKDQIVDGSYMKPTHTHDPHHVMDQDYFLASAIVAPRNVADVQSIVGLANKFSFPLWPISI

Target ASNLIVRDGG---IRDVVIML-TEMKEI-KVA--GTTMIVDAGAKLIDTTYEALAADLTG-FEFACGIP--GSVGGAVYM
1w1l.1.A GRNSGYGGAAPRVSGSVVLDMGKNMNRVLEVNVEGAYCVVEPGVTYHDLHNYLEANNLRDKLWLDVPDLGGGSVLGNAVE

Target NAGAYG--GEIKDVFQSAEVLLADGTIQTMTK-----------------EDLNFRYRHSEI------------QELHCIV
1w1l.1.A RGVGYTPYGDHWMMHSGMEVVLANGELLRTGMGALPDPKRPETMGLKPEDQPWSKIAHLFPYGFGPYIDGLFSQSNMGIV

Target LQATFALEKGNHA---------EIKAQMDELTELRELKQPLEYPSCGSVFKRPVGHFTGKLIQDAGL---QGL--KW-G-
1w1l.1.A TKIGIWLMPNPRGYQSYLITLPKDGDLKQAVDIIRPLRL------------GMALQNVPTIRHILLDAAVLGDKRSYSSR

Target GAQISE------------KHAGFIVNIDHATATDYVELIAHIQEVIKEKFDVELQTEVRIIGEEV
1w1l.1.A TEPLSDEELDKIAKQLNLGRWNFYGALYG-PEPIRRVLWETIKDAFSAIPGV-------------




Model #03

FileBuilt withOligo-StateLigandsGMQEQMEAN
PDB ProMod3 Version 1.0.2. MONOMER
None
0.37-5.22
QMEAN-5.22
-1.39
All Atom-3.15
Solvation-1.05
Torsion-4.42
TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
3s1f.1.A14.74monomerHHblitsX-ray2.00Å0.27 3 - 195 0.63Cytokinin dehydrogenase 1
LigandAdded to ModelDescription
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
GOL✕ - Not biologically relevant.
GLYCEROL
GOL✕ - Not biologically relevant.
GLYCEROL
GOL✕ - Not biologically relevant.
GLYCEROL
GOL✕ - Not biologically relevant.
GLYCEROL
GOL✕ - Not biologically relevant.
GLYCEROL
GOL✕ - Not biologically relevant.
GLYCEROL
GOL✕ - Not biologically relevant.
GLYCEROL
GOL✕ - Not biologically relevant.
GLYCEROL
NAG✕ - Binding site not conserved.
SUGAR (N-ACETYL-D-GLUCOSAMINE)
NAG✕ - Binding site not conserved.
SUGAR (N-ACETYL-D-GLUCOSAMINE)
NAG✕ - Binding site not conserved.
SUGAR (N-ACETYL-D-GLUCOSAMINE)
NAG✕ - Binding site not conserved.
SUGAR (2-MER)
PEG✕ - Not biologically relevant.
DI(HYDROXYETHYL)ETHER
ZIP✕ - Binding site not conserved.
N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE

Target    MNTKAMLETLNEITLLVDE-PLKNVTF-T--KTGGPADVLALPKTKKEVEEIVAYCREQ---GLSWLVLGNASNLIVRDG
3s1f.1.A --PASLAALALDGKLRTDSNATAAASTDFGNITSALPAAVLYPSSTADLVALLSAANSTPGWPYTIAFRGRGHSLMGQAF

Target GIRDVVIMLTEMK------EIKVA--GTTMIVDAGAKLIDTTYEALAADLTGFEFACGIP-GSVGGAVYMNAGA----YG
3s1f.1.A APGGVVVNMASLGDAAAPPRINVSADGRYVDAGGEQVWIDVLRASLARGVAP-RSWTEYLYLTVGGTLSNAGISGQAFRH

Target GEIKDVFQSAEVLLADGTIQTMTK---EDLNFRYRHSEIQELHCIVLQATFALEKGNHAEIKAQMDELTELRELKQPLEY
3s1f.1.A GPQISNVLEMDVITGHGEMVTCSKQLNADLFDAVLGGL--GQFGVITRARIAVEPAPA----------------------

Target PSCGSVFKRPVGHFTGKLIQDAGLQGLKWGGAQISEKHAGFIVNIDHATATDYVELIAHIQEVIKEKFDVELQTEVRIIG
3s1f.1.A --------------------------------------------------------------------------------

Target EEV
3s1f.1.A ---




Materials and Methods

Template Search

Template search with Blast and HHBlits has been performed against the SWISS-MODEL template library (SMTL, last update: 2017-10-11, last included PDB release: 2017-10-06).

The target sequence was searched with BLAST (Altschul et al., 1997) against the primary amino acid sequence contained in the SMTL. A total of 15 templates were found.

An initial HHblits profile has been built using the procedure outlined in (Remmert, et al., 2011), followed by 1 iteration of HHblits against NR20. The obtained profile has then be searched against all profiles of the SMTL. A total of 139 templates were found.

Template Selection

For each identified template, the template's quality has been predicted from features of the target-template alignment. The templates with the highest quality have then been selected for model building.

Model Building

Models are built based on the target-template alignment using ProMod3. Coordinates which are conserved between the target and the template are copied from the template to the model. Insertions and deletions are remodelled using a fragment library. Side chains are then rebuilt. Finally, the geometry of the resulting model is regularized by using a force field. In case loop modelling with ProMod3 fails, an alternative model is built with PROMOD-II (Guex, et al., 1997).

Model Quality Estimation

The global and per-residue model quality has been assessed using the QMEAN scoring function (Benkert, et al., 2011) . For improved performance, weights of the individual QMEAN terms have been trained specifically for SWISS-MODEL.

Ligand Modelling

Ligands present in the template structure are transferred by homology to the model when the following criteria are met (Gallo -Casserino, to be published): (a) The ligands are annotated as biologically relevant in the template library, (b) the ligand is in contact with the model, (c) the ligand is not clashing with the protein, (d) the residues in contact with the ligand are conserved between the target and the template. If any of these four criteria is not satisfied, a certain ligand will not be included in the model. The model summary includes information on why and which ligand has not been included.

Oligomeric State Conservation

Homo-oligomeric structure of the target protein is predicted based on the analysis of pairwise interfaces of the identified template structures. For each relevant interface between polypeptide chains (interfaces with more than 10 residue-residue interactions), the QscoreOligomer (Mariani et al., 2011) is predicted from features such as similarity to target and frequency of observing this interface in the identified templates (Kiefer, Bertoni, Biasini, to be published). The prediction is performed with a random forest regressor using these features as input parameters to predict the probability of conservation for each interface. The QscoreOligomer of the whole complex is then calculated as the weight-averaged QscoreOligomer of the interfaces. The oligomeric state of the target is predicted to be the same as in the template when QscoreOligomer is predicted to be higher or equal to 0.5.

References

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25, 3389-3402.
Remmert, M., Biegert, A., Hauser, A. and Soding, J. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods, 9, 173-175.
Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
Sali, A. and Blundell, T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol, 234, 779-815.
Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350.
Mariani, V., Kiefer, F., Schmidt, T., Haas, J. and Schwede, T. (2011) Assessment of template based protein structure predictions in CASP9. Proteins, 79 Suppl 10, 37-58.

Table T1:

Primary amino acid sequence for which templates were searched and models were built.

MNTKAMLETLNEITLLVDEPLKNVTFTKTGGPADVLALPKTKKEVEEIVAYCREQGLSWLVLGNASNLIVRDGGIRDVVIMLTEMKEIKVAGTTMIVDAG
AKLIDTTYEALAADLTGFEFACGIPGSVGGAVYMNAGAYGGEIKDVFQSAEVLLADGTIQTMTKEDLNFRYRHSEIQELHCIVLQATFALEKGNHAEIKA
QMDELTELRELKQPLEYPSCGSVFKRPVGHFTGKLIQDAGLQGLKWGGAQISEKHAGFIVNIDHATATDYVELIAHIQEVIKEKFDVELQTEVRIIGEEV

Table T2:

TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityCoverageDescription
3tx1.1.A56.08monomerHHblitsX-ray2.69Å0.450.99UDP-N-acetylenolpyruvoylglucosamine reductase
1hsk.1.A52.54monomerHHblitsX-ray2.30Å0.440.98UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE
3tx1.1.A57.84monomerBLASTX-ray2.69Å0.460.96UDP-N-acetylenolpyruvoylglucosamine reductase
4pyt.1.A42.32monomerBLASTX-ray1.85Å0.400.98UDP-N-acetylenolpyruvoylglucosamine reductase
4pyt.1.A42.66monomerHHblitsX-ray1.85Å0.410.95UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.A28.28homo-dimerHHblitsX-ray2.20Å0.330.97UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.B28.28homo-dimerHHblitsX-ray2.20Å0.330.97UDP-N-acetylenolpyruvoylglucosamine reductase
3i99.1.A28.62monomerHHblitsX-ray2.20Å0.330.94UDP-N-acetylenolpyruvoylglucosamine reductase
4jay.1.A29.29monomerHHblitsX-ray2.23Å0.330.93UDP-N-acetylenolpyruvoylglucosamine reductase
4jb1.1.A29.29monomerHHblitsX-ray2.10Å0.330.93UDP-N-acetylenolpyruvoylglucosamine reductase
1mbb.1.A27.60monomerHHblitsX-ray2.30Å0.330.93URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1mbt.1.A27.60monomerHHblitsX-ray3.00Å0.330.93URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2q85.1.A27.60monomerHHblitsX-ray2.51Å0.330.93UDP-N-acetylenolpyruvoylglucosamine reductase
2mbr.1.A27.70monomerHHblitsX-ray1.80Å0.330.93URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1uxy.1.A27.34monomerHHblitsX-ray1.80Å0.330.93URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2gqu.1.A38.40monomerHHblitsX-ray1.60Å0.370.88UDP-N-Acetylenolpyruvylglucosamine Reductase
2gqt.1.A38.40monomerHHblitsX-ray1.30Å0.370.88UDP-N-Acetylenolpyruvylglucosamine Reductase
4jay.1.A33.20monomerBLASTX-ray2.23Å0.360.85UDP-N-acetylenolpyruvoylglucosamine reductase
4jb1.1.A33.20monomerBLASTX-ray2.10Å0.360.85UDP-N-acetylenolpyruvoylglucosamine reductase
2gqu.1.A39.59monomerBLASTX-ray1.60Å0.380.82UDP-N-Acetylenolpyruvylglucosamine Reductase
2gqt.1.A39.59monomerBLASTX-ray1.30Å0.380.82UDP-N-Acetylenolpyruvylglucosamine Reductase
2mbr.1.A33.61monomerBLASTX-ray1.80Å0.360.81URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1mbb.1.A33.61monomerBLASTX-ray2.30Å0.360.81URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1mbt.1.A33.61monomerBLASTX-ray3.00Å0.360.81URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2q85.1.A33.61monomerBLASTX-ray2.51Å0.360.81UDP-N-acetylenolpyruvoylglucosamine reductase
1uxy.1.A33.20monomerBLASTX-ray1.80Å0.360.81URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2uuu.1.A14.02homo-dimerHHblitsX-ray1.95Å0.270.90ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE
2uuv.2.B14.02homo-dimerHHblitsX-ray1.99Å0.270.90ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE
1w1l.1.A15.87homo-dimerHHblitsX-ray2.70Å0.260.90VANILLYL-ALCOHOL OXIDASE
5jzx.1.A33.33homo-dimerBLASTX-ray2.20Å0.360.79UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.B33.33homo-dimerBLASTX-ray2.20Å0.360.79UDP-N-acetylenolpyruvoylglucosamine reductase
2q4w.1.A12.08monomerHHblitsX-ray1.70Å0.260.88Cytokinin dehydrogenase 7
3i99.1.A39.01monomerBLASTX-ray2.20Å0.370.61UDP-N-acetylenolpyruvoylglucosamine reductase
1f0x.1.A11.76monomerHHblitsX-ray1.90Å0.260.68D-LACTATE DEHYDROGENASE
3pm9.1.A23.56homo-dimerHHblitsX-ray2.57Å0.310.64Putative oxidoreductase
1e8g.1.A18.23homo-octamerHHblitsX-ray2.10Å0.280.64VANILLYL-ALCOHOL OXIDASE
1w1m.1.A17.71homo-dimerHHblitsX-ray3.00Å0.280.64VANILLYL-ALCOHOL OXIDASE
1w1k.1.A17.71homo-dimerHHblitsX-ray2.55Å0.280.64VANILLYL-ALCOHOL OXIDASE
1w1j.1.A17.71homo-dimerHHblitsX-ray2.70Å0.280.64VANILLYL-ALCOHOL OXIDASE
5mxj.1.A17.71homo-octamerHHblitsX-ray2.80Å0.280.64Vanillyl-alcohol oxidase
1dzn.1.A17.71homo-octamerHHblitsX-ray2.80Å0.280.64VANILLYL-ALCOHOL OXIDASE
1ahv.1.A17.71homo-octamerHHblitsX-ray3.10Å0.280.64VANILLYL-ALCOHOL OXIDASE
1ahu.1.A17.71homo-octamerHHblitsX-ray2.70Å0.280.64VANILLYL-ALCOHOL OXIDASE
5mxu.1.A17.71homo-octamerHHblitsX-ray2.80Å0.280.64Vanillyl-alcohol oxidase
1e0y.1.A18.32homo-dimerHHblitsX-ray2.75Å0.280.64VANILLYL-ALCOHOL OXIDASE
1qlt.1.A17.71homo-octamerHHblitsX-ray2.20Å0.280.64VANILLYL-ALCOHOL OXIDASE
1diq.1.A16.67hetero-oligomerHHblitsX-ray2.75Å0.270.64P-CRESOL METHYLHYDROXYLASE
1wve.1.A16.67hetero-oligomerHHblitsX-ray1.85Å0.270.644-cresol dehydrogenase [hydroxylating] flavoprotein subunit
4o95.1.A17.37monomerHHblitsX-ray1.75Å0.280.63Cytokinin dehydrogenase 4
5hhz.1.A17.37monomerHHblitsX-ray2.00Å0.280.63Cytokinin dehydrogenase 4
5fxd.1.A16.15homo-dimerHHblitsX-ray1.70Å0.260.64PROBABLE VANILLYL-ALCOHOL OXIDASE
3dq0.1.A14.74monomerHHblitsX-ray1.90Å0.270.63Cytokinin dehydrogenase 1
4ml8.1.A14.81monomerHHblitsX-ray2.70Å0.270.63Cytokinin oxidase 2
3s1f.1.A14.74monomerHHblitsX-ray2.00Å0.270.63Cytokinin dehydrogenase 1
2qpm.1.A15.05monomerHHblitsX-ray1.85Å0.270.62Cytokinin dehydrogenase 1
3kjm.1.A15.05monomerHHblitsX-ray1.90Å0.270.62Cytokinin dehydrogenase 1
3s1e.1.A15.14monomerHHblitsX-ray1.90Å0.270.62Cytokinin dehydrogenase 1
1w1q.1.A15.14monomerHHblitsX-ray1.80Å0.270.62CYTOKININ DEHYDROGENASE 1
3s1d.1.A15.22monomerHHblitsX-ray1.75Å0.270.61Cytokinin dehydrogenase 1
4bby.1.A16.67homo-dimerHHblitsX-ray1.90Å0.280.60ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
4bca.1.A16.67homo-dimerHHblitsX-ray2.40Å0.280.60ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
4bc7.1.A16.76homo-dimerHHblitsX-ray2.40Å0.280.60ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
4f4q.1.A21.51monomerHHblitsX-ray2.62Å0.300.57DprE1
4aut.1.A21.51monomerHHblitsX-ray2.10Å0.300.57DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE
4p8c.1.A20.93monomerHHblitsX-ray1.95Å0.290.57Probable decaprenylphosphoryl-beta-D-ribose oxidase
4p8c.2.A20.93monomerHHblitsX-ray1.95Å0.290.57Probable decaprenylphosphoryl-beta-D-ribose oxidase
4p8m.1.A20.93monomerHHblitsX-ray2.09Å0.290.57Probable decaprenylphosphoryl-beta-D-ribose oxidase
4fdp.1.A21.05monomerHHblitsX-ray2.23Å0.290.57oxidoreductase DprE1
4fdp.2.A21.05monomerHHblitsX-ray2.23Å0.290.57oxidoreductase DprE1
4ncr.1.A21.05monomerHHblitsX-ray1.88Å0.290.57decaprenylphosphoryl-beta-D-ribose oxidase
3hsu.1.A21.34monomerHHblitsX-ray1.69Å0.300.55Glucooligosaccharide oxidase
2axr.1.A21.34monomerHHblitsX-ray1.98Å0.300.55glucooligosaccharide oxidase
4kw5.1.A21.34monomerHHblitsX-ray2.61Å0.300.55Oxidoreductase
3w8w.1.A23.78homo-dimerHHblitsX-ray1.95Å0.290.55Putative FAD-dependent oxygenase EncM
4xlo.1.A23.78homo-dimerHHblitsX-ray1.67Å0.290.55FAD-dependent oxygenase EncM
5k8e.1.A21.34monomerHHblitsX-ray1.93Å0.290.55FAD linked oxidase-like protein
3vte.1.A22.09monomerHHblitsX-ray2.75Å0.290.54Tetrahydrocannabinolic acid synthase
4dns.1.A22.70monomerHHblitsX-ray2.15Å0.290.54FAD-linked oxidoreductase BG60
3fwa.1.A17.68monomerHHblitsX-ray1.50Å0.280.55Reticuline oxidase
2vfs.1.A21.25monomerHHblitsX-ray1.60Å0.300.53XYLITOL OXIDASE
3fw8.1.A18.40monomerHHblitsX-ray1.50Å0.280.54Reticuline oxidase
3fw7.1.A18.40monomerHHblitsX-ray1.82Å0.280.54Reticuline oxidase
1i19.1.A18.52monomerHHblitsX-ray1.70Å0.290.54CHOLESTEROL OXIDASE
2bvg.1.A20.25monomerHHblitsX-ray3.18Å0.280.546-HYDROXY-D-NICOTINE OXIDASE
3gsy.1.A18.40monomerHHblitsX-ray1.63Å0.280.54Reticuline oxidase; Berberine bridge-forming enzyme
3tsh.1.A20.25monomerHHblitsX-ray1.90Å0.280.54Pollen allergen Phl p 4
4pvk.1.A20.25monomerHHblitsX-ray1.30Å0.280.54Pollen allergen Phl p 4.0202
4pvh.1.A20.25monomerHHblitsX-ray1.40Å0.280.54Pollen allergen Phl p 4.0202
4pvj.1.A20.25monomerHHblitsX-ray1.80Å0.280.54Pollen allergen Phl p 4.0202
3fw9.1.A18.52monomerHHblitsX-ray1.49Å0.290.54Reticuline oxidase
3d2j.1.A18.52monomerHHblitsX-ray2.05Å0.290.54berberine bridge-forming enzyme
2ipi.1.A20.50monomerHHblitsX-ray1.65Å0.290.54Aclacinomycin oxidoreductase (AknOx)
4pve.1.A20.25monomerHHblitsX-ray1.50Å0.280.54Pollen allergen Phl p 4.0202
3js8.1.A15.43monomerHHblitsX-ray1.54Å0.280.54Cholesterol oxidase
4ec3.1.A18.52monomerHHblitsX-ray2.65Å0.280.54Reticuline oxidase
2wdw.1.A17.39homo-dimerHHblitsX-ray3.21Å0.290.54PUTATIVE HEXOSE OXIDASE
5awv.1.C17.39homo-tetramerHHblitsX-ray1.93Å0.290.54Putative hexose oxidase
5i1v.1.A19.25homo-dimerHHblitsX-ray1.84Å0.290.54CrmK
2i0k.1.A18.01monomerHHblitsX-ray1.60Å0.290.54Oxidoreductase
4pzf.1.A17.18monomerHHblitsX-ray2.20Å0.280.54Reticuline oxidase
3rj8.1.A18.29monomerHHblitsX-ray2.40Å0.270.55Carbohydrate oxidase
2y3r.1.A18.63homo-dimerHHblitsX-ray1.79Å0.290.54TAML
4ud8.1.A18.52monomerHHblitsX-ray2.09Å0.280.54FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
4ud8.2.A18.52monomerHHblitsX-ray2.09Å0.280.54FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
3pqb.1.A19.88homo-dimerHHblitsX-ray2.32Å0.280.54Putative oxidoreductase
5d79.1.A19.88monomerHHblitsX-ray1.85Å0.280.54Berberine bridge enzyme-like protein
4uhw.1.A14.01homo-dimerHHblitsX-ray2.60Å0.270.52ALDEHYDE OXIDASE
3b9j.1.B12.74hetero-oligomerHHblitsX-ray2.30Å0.270.52xanthine oxidase
4ytz.1.A11.46homo-dimerHHblitsX-ray2.30Å0.270.52Xanthine dehydrogenase/oxidase
4ytz.1.B11.46homo-dimerHHblitsX-ray2.30Å0.270.52Xanthine dehydrogenase/oxidase
4ysw.1.B11.46homo-dimerHHblitsX-ray1.99Å0.270.52Xanthine dehydrogenase/oxidase
1fiq.1.B12.66hetero-oligomerHHblitsX-ray2.50Å0.260.53XANTHINE OXIDASE
1n5x.1.A13.46homo-dimerHHblitsX-ray2.80Å0.270.52Xanthine Dehydrogenase
3amz.1.A13.46homo-dimerHHblitsX-ray2.10Å0.270.52Xanthine dehydrogenase/oxidase
3ax7.1.A13.46homo-dimerHHblitsX-ray2.34Å0.270.52Xanthine dehydrogenase/oxidase
2e1q.1.A12.82homo-dimerHHblitsX-ray2.60Å0.270.52Xanthine dehydrogenase/oxidase
3sr6.1.B12.74hetero-oligomerHHblitsX-ray2.10Å0.260.52Xanthine dehydrogenase/oxidase
3uni.1.A13.55homo-dimerHHblitsX-ray2.20Å0.270.52Xanthine dehydrogenase/oxidase
3zyv.1.A11.46homo-dimerHHblitsX-ray2.55Å0.260.52AOX3
3nvv.1.B12.90hetero-oligomerHHblitsX-ray1.82Å0.270.52Xanthine dehydrogenase/oxidase
2ckj.1.A12.90homo-dimerHHblitsX-ray3.59Å0.270.52XANTHINE OXIDOREDUCTASE
2e3t.1.A11.54homo-dimerHHblitsX-ray2.28Å0.260.52Xanthine dehydrogenase/oxidase
2e3t.1.B11.54homo-dimerHHblitsX-ray2.28Å0.260.52Xanthine dehydrogenase/oxidase
3hrd.1.C16.56hetero-oligomerHHblitsX-ray2.20Å0.290.50Nicotinate dehydrogenase FAD-subunit
1wyg.1.A10.97monomerHHblitsX-ray2.60Å0.260.52Xanthine dehydrogenase/oxidase
1zxi.1.C16.56hetero-oligomerHHblitsX-ray1.70Å0.280.50Carbon monoxide dehydrogenase medium chain
3an1.1.A10.97homo-dimerHHblitsX-ray1.73Å0.260.52Xanthine dehydrogenase/oxidase
5epg.1.A15.03homo-dimerHHblitsX-ray3.39Å0.270.51Aldehyde oxidase
1ffv.1.C13.82hetero-oligomerHHblitsX-ray2.25Å0.270.51CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
1n62.1.C16.67hetero-oligomerHHblitsX-ray1.09Å0.280.50Carbon monoxide dehydrogenase medium chain
1ffu.1.C15.33hetero-oligomerHHblitsX-ray2.35Å0.280.50CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
1t3q.1.C12.08hetero-oligomerHHblitsX-ray1.80Å0.280.50quinoline 2-oxidoreductase medium subunit
2w3r.1.A14.00hetero-oligomerHHblitsX-ray2.90Å0.270.50XANTHINE DEHYDROGENASE
1jro.1.A14.09hetero-oligomerHHblitsX-ray2.70Å0.270.50xanthine dehydrogenase, chain A
4zoh.1.B10.88hetero-oligomerHHblitsX-ray2.20Å0.260.49Putative oxidoreductase FAD-binding subunit
4g3t.1.A27.43monomerHHblitsX-ray2.35Å0.320.38oxidoreductase DprE1
1sb3.1.B22.22hetero-oligomerHHblitsX-ray2.20Å0.300.334-hydroxybenzoyl-CoA reductase beta subunit
2yvs.1.A13.86homo-dimerHHblitsX-ray2.00Å0.260.34Glycolate oxidase subunit GlcE
2yvs.1.B13.86homo-dimerHHblitsX-ray2.00Å0.260.34Glycolate oxidase subunit GlcE
1wn2.1.A16.22homo-dimerHHblitsX-ray1.20Å0.280.12Peptidyl-tRNA hydrolase
2d3k.1.A16.22homo-dimerHHblitsX-ray1.90Å0.280.12Peptidyl-tRNA hydrolase
2zv3.1.A22.22homo-dimerHHblitsX-ray2.10Å0.290.12Peptidyl-tRNA hydrolase
2zv3.3.B22.22homo-dimerHHblitsX-ray2.10Å0.290.12Peptidyl-tRNA hydrolase
2zv3.4.A22.22homo-dimerHHblitsX-ray2.10Å0.290.12Peptidyl-tRNA hydrolase
2zv3.4.B22.22homo-dimerHHblitsX-ray2.10Å0.290.12Peptidyl-tRNA hydrolase
1rlk.1.A13.51monomerHHblitsX-ray1.95Å0.260.12Hypothetical protein Ta0108
1q7s.1.A13.89monomerHHblitsX-ray2.00Å0.280.12bit1
1q7s.2.A13.89monomerHHblitsX-ray2.00Å0.280.12bit1
1xty.1.A8.11homo-dimerHHblitsX-ray1.80Å0.250.12Peptidyl-tRNA hydrolase
3erj.1.A20.00homo-dimerHHblitsX-ray1.80Å0.260.12Peptidyl-tRNA hydrolase
3erj.1.B20.00homo-dimerHHblitsX-ray1.80Å0.260.12Peptidyl-tRNA hydrolase
1rzw.1.A20.00monomerHHblitsNMRNA0.260.12Protein AF2095(GR4)
5d88.1.A34.48homo-dimerHHblitsX-ray1.66Å0.330.10Predicted protease of the collagenase family