SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "A0A0M2AJC3-MurB-E-faecium" submitted to SWISS-MODEL workspace on Oct. 17, 2017, 3:45 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 157 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
0.78-0.43
QMEAN-0.43
0.83
All Atom-0.42
Solvation0.21
Torsion-0.61
TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
3tx1.1.A57.64monomerBLASTX-ray2.69Å0.46 13 - 300 0.93UDP-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    MNKEEIVESLATITLLFDEPLMNYTFTKTGGPADVLAFPKKQEEVKQIIDYCRIHDIPWMVLGNASNLIVQDGGIRGVVI
3tx1.1.A ------------IAIKLNEPLSKYTYTKTGGAADVFVMPKTIEEAQEVVAYCHQNKIPLTILGNGSNLIIKDGGIRGVIL

Target MLTEMKQIHVKGTMVIAEAGASLIDTTYAALAESLTGFEFACGIPGSVGGAVYMNAGAYGGEIKDVFAEVDLLLEDGTLK
3tx1.1.A HLDLLQTIERNNTQIVAMSGAKLIDTAKFALNESLSGLEFACGIPGSIGGALHMNAGAYGGEISDVLEAATVLTQTGELK

Target TLTKDEMVFSYRHSKVQELRAIVLEARFSLQTGDYEAIKARMDELTELRQSKQPLEYPSCGSVFKRPVGHYTGQLIQQAG
3tx1.1.A KLKRSELKAAYRFSTIAEKNYIVLDATFSLALEEKNLIQAKMDELTAAREAKQPLEYPSCGSVFKRPPGHFAGKLIQDSG

Target LQGLKWGGAQVSEKHAGFIVNIDHATATDYIELIAHIQEVIKEKFDVSLETEVRIIGEKQAISETSRSLAN
3tx1.1.A LQGHIIGGAQVSLKHAGFIVNIGGATATDYMNLIAYVQQTVREKFDVELETEVKIIGEDK-----------




Model #02

FileBuilt withOligo-StateLigandsGMQEQMEAN
PDB ProMod3 Version 1.0.2. MONOMER
None
0.58-2.57
QMEAN-2.57
-1.67
All Atom-2.89
Solvation-1.29
Torsion-1.95
TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
1uxy.1.A33.72monomerBLASTX-ray1.80Å0.36 43 - 303 0.83URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
LigandAdded to ModelDescription
EPU✕ - Binding site not conserved.
URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE

Target    MNKEEIVESLATITLLFDEPLMNYTFTKTGGPADVLAFPKKQEEVKQIID---YCRIHDIPWMVLGNASN-LIVQDGGIR
1uxy.1.A ------------------------------------------EDEQQLLNAWQYATAEGQPVLILGEGSNVLFLED--YR

Target GVVIMLTEMKQIHVK----GTMVIAEAGASLIDTTYAALAESLTGFEFACGIPGSVGGAVYMNAGAYGGEIKDVFAEVDL
1uxy.1.A GTVI-INRIKGIEIHDEPDAWYLHVGAGENWHRLVKYTLQEGMPGLENLALIPGCVGSSPIQNIGAYGVELQRVCAYVDS

Target L-LEDGTLKTLTKDEMVFSYRHS----KVQELRAIVL-------EARFSLQTGDYEAIKAR-------MDELTELRQSK-
1uxy.1.A VELATGKQVRLTAKECRFGYRDSIFKHEYQDRFAIVAVGLRLPKEWQPVLTYGDLTRLDPTTVTPQQVFNAVCHMRTTKL

Target -QPLEYPSCGSVFKRPV----------GHYTGQLIQQAGLQGLK----W------------GGAQVSEKHAGFIVNIDHA
1uxy.1.A PDPKVNGNAGAFFKNPVVSAETAKALLSQFPTAPNYPQADGSVKLAAGWLIDQCQLKGMQIGGAAVHRQQALVLINEDNA

Target TATDYIELIAHIQEVIKEKFDVSLETEVRIIGEKQAISETSRSLAN
1uxy.1.A KSEDVVQLAHHVRQKVGEKFNVWLEPEVRFIGASGEVS--------




Model #03

FileBuilt withOligo-StateLigandsGMQEQMEAN
PDB ProMod3 Version 1.0.2. MONOMER (matching prediction)
None
0.47-6.74
QMEAN-6.74
-2.05
All Atom-2.32
Solvation-1.20
Torsion-6.42
TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
5mxu.1.A14.87homo-octamerHHblitsX-ray2.80Å0.27 3 - 284 0.86Vanillyl-alcohol oxidase
LigandAdded to ModelDescription
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
FAD✕ - Binding site not conserved.
FLAVIN-ADENINE DINUCLEOTIDE
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

Target    MNKEEIVESLATI----TLL--------FDE-PLMNYTF---TK----TGGPADVLAFPKKQEEVKQIIDYCRIHDIPWM
5mxu.1.A --FNEFIQDIIRIVGSENVEVISSKDQIVDGSYMKPTHTHDPHHVMDQDYFLASAIVAPRNVADVQSIVGLANKFSFPLW

Target VLGNASNLIVQDG---GIRGVVIML-TEMKQI-HVK--GTMVIAEAGASLIDTTYAALAESLTG-FEFACGIP--GSVGG
5mxu.1.A PISIGRNSGYGGAAPRVSGSVVLDMGKNMNRVLEVNVEGAYCVVEPGVTYHDLHNYLEANNLRDKLWLDVPDLGGGSVLG

Target AVYMNAGAYG--GEIKDVFAEVDLLLEDGTLKTLTK-----------------DEMVFSYRHSKVQ----------EL--
5mxu.1.A NAVERGVGYTPYGDHWMMHSGMEVVLANGELLRTGMGALPDPKRPETMGLKPEDQPWSKIAHLFPYGFGPYIDGLFSQSN

Target RAIVLEARFSLQTGDYE---------AIKARMDELTELRQSKQPLEYPSCGSVFKRPVGHYTGQLIQQA---GLQGLK--
5mxu.1.A MGIVTKIGIWLMPNPRGYQSYLITLPKDGDLKQAVDIIRPLRL------------GMALQNVPTIRHILLDAAVLGDKRS

Target WGG--AQVSE------------KHAGFIVNIDHATATDYIELIAHIQEVIKEKFDVSLETEVRIIGEKQAISETSRSLAN
5mxu.1.A YSSRTEPLSDEELDKIAKQLNLGRWNFYGALYG-PEPIRRVLWETIKDAFSAI---------------------------




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 142 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.

MNKEEIVESLATITLLFDEPLMNYTFTKTGGPADVLAFPKKQEEVKQIIDYCRIHDIPWMVLGNASNLIVQDGGIRGVVIMLTEMKQIHVKGTMVIAEAG
ASLIDTTYAALAESLTGFEFACGIPGSVGGAVYMNAGAYGGEIKDVFAEVDLLLEDGTLKTLTKDEMVFSYRHSKVQELRAIVLEARFSLQTGDYEAIKA
RMDELTELRQSKQPLEYPSCGSVFKRPVGHYTGQLIQQAGLQGLKWGGAQVSEKHAGFIVNIDHATATDYIELIAHIQEVIKEKFDVSLETEVRIIGEKQ
AISETSRSLAN

Table T2:

TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityCoverageDescription
1hsk.1.A51.80monomerHHblitsX-ray2.30Å0.440.98UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE
3tx1.1.A57.19monomerHHblitsX-ray2.69Å0.460.94UDP-N-acetylenolpyruvoylglucosamine reductase
3tx1.1.A57.64monomerBLASTX-ray2.69Å0.460.93UDP-N-acetylenolpyruvoylglucosamine reductase
1hsk.1.A54.80monomerBLASTX-ray2.30Å0.450.90UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE
4pyt.1.A44.90monomerBLASTX-ray1.85Å0.410.95UDP-N-acetylenolpyruvoylglucosamine reductase
4pyt.1.A45.30monomerHHblitsX-ray1.85Å0.420.92UDP-N-acetylenolpyruvoylglucosamine reductase
3i99.1.A29.66monomerHHblitsX-ray2.20Å0.340.93UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.A28.97homo-dimerHHblitsX-ray2.20Å0.330.93UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.B28.97homo-dimerHHblitsX-ray2.20Å0.330.93UDP-N-acetylenolpyruvoylglucosamine reductase
1mbb.1.A29.47monomerHHblitsX-ray2.30Å0.340.92URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1mbt.1.A29.47monomerHHblitsX-ray3.00Å0.340.92URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2q85.1.A29.47monomerHHblitsX-ray2.51Å0.340.92UDP-N-acetylenolpyruvoylglucosamine reductase
2mbr.1.A29.58monomerHHblitsX-ray1.80Å0.340.91URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1uxy.1.A29.23monomerHHblitsX-ray1.80Å0.340.91URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
4jay.1.A29.79monomerHHblitsX-ray2.23Å0.340.91UDP-N-acetylenolpyruvoylglucosamine reductase
4jb1.1.A29.79monomerHHblitsX-ray2.10Å0.340.91UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.A31.07homo-dimerBLASTX-ray2.20Å0.340.90UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.B31.07homo-dimerBLASTX-ray2.20Å0.340.90UDP-N-acetylenolpyruvoylglucosamine reductase
2gqu.1.A38.02monomerHHblitsX-ray1.60Å0.370.85UDP-N-Acetylenolpyruvylglucosamine Reductase
2gqt.1.A38.02monomerHHblitsX-ray1.30Å0.370.85UDP-N-Acetylenolpyruvylglucosamine Reductase
1mbb.1.A34.11monomerBLASTX-ray2.30Å0.360.83URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1mbt.1.A34.11monomerBLASTX-ray3.00Å0.360.83URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2q85.1.A34.11monomerBLASTX-ray2.51Å0.360.83UDP-N-acetylenolpyruvoylglucosamine reductase
2mbr.1.A34.11monomerBLASTX-ray1.80Å0.360.83URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1uxy.1.A33.72monomerBLASTX-ray1.80Å0.360.83URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
4jay.1.A31.15monomerBLASTX-ray2.23Å0.340.84UDP-N-acetylenolpyruvoylglucosamine reductase
4jb1.1.A31.15monomerBLASTX-ray2.10Å0.340.84UDP-N-acetylenolpyruvoylglucosamine reductase
2uuu.1.A14.29homo-dimerHHblitsX-ray1.95Å0.280.90ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE
2uuv.2.B14.29homo-dimerHHblitsX-ray1.99Å0.280.90ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE
2gqu.1.A39.75monomerBLASTX-ray1.60Å0.380.78UDP-N-Acetylenolpyruvylglucosamine Reductase
2gqt.1.A39.75monomerBLASTX-ray1.30Å0.380.78UDP-N-Acetylenolpyruvylglucosamine Reductase
3i99.1.A35.34monomerBLASTX-ray2.20Å0.370.80UDP-N-acetylenolpyruvoylglucosamine reductase
1w1l.1.A14.29homo-dimerHHblitsX-ray2.70Å0.270.88VANILLYL-ALCOHOL OXIDASE
5mxu.1.A14.87homo-octamerHHblitsX-ray2.80Å0.270.86Vanillyl-alcohol oxidase
1dzn.1.A14.87homo-octamerHHblitsX-ray2.80Å0.270.86VANILLYL-ALCOHOL OXIDASE
1qlt.1.A14.18homo-octamerHHblitsX-ray2.20Å0.260.86VANILLYL-ALCOHOL OXIDASE
2q4w.1.A13.69monomerHHblitsX-ray1.70Å0.260.85Cytokinin dehydrogenase 7
4bc7.1.A10.93homo-dimerHHblitsX-ray2.40Å0.270.79ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
4bby.1.A10.93homo-dimerHHblitsX-ray1.90Å0.270.79ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
1f0x.1.A16.13monomerHHblitsX-ray1.90Å0.270.70D-LACTATE DEHYDROGENASE
3pm9.1.A21.15homo-dimerHHblitsX-ray2.57Å0.290.67Putative oxidoreductase
1e8g.1.A17.62homo-octamerHHblitsX-ray2.10Å0.280.62VANILLYL-ALCOHOL OXIDASE
1w1m.1.A17.10homo-dimerHHblitsX-ray3.00Å0.280.62VANILLYL-ALCOHOL OXIDASE
1w1k.1.A17.10homo-dimerHHblitsX-ray2.55Å0.280.62VANILLYL-ALCOHOL OXIDASE
1w1j.1.A17.10homo-dimerHHblitsX-ray2.70Å0.280.62VANILLYL-ALCOHOL OXIDASE
5mxj.1.A17.10homo-octamerHHblitsX-ray2.80Å0.280.62Vanillyl-alcohol oxidase
1ahv.1.A17.10homo-octamerHHblitsX-ray3.10Å0.280.62VANILLYL-ALCOHOL OXIDASE
1ahu.1.A17.10homo-octamerHHblitsX-ray2.70Å0.280.62VANILLYL-ALCOHOL OXIDASE
1e0y.1.A16.67homo-dimerHHblitsX-ray2.75Å0.280.62VANILLYL-ALCOHOL OXIDASE
4o95.1.A16.23monomerHHblitsX-ray1.75Å0.280.61Cytokinin dehydrogenase 4
5hhz.1.A16.23monomerHHblitsX-ray2.00Å0.280.61Cytokinin dehydrogenase 4
4ml8.1.A13.76monomerHHblitsX-ray2.70Å0.280.61Cytokinin oxidase 2
1w1q.1.A18.38monomerHHblitsX-ray1.80Å0.290.59CYTOKININ DEHYDROGENASE 1
3dq0.1.A18.48monomerHHblitsX-ray1.90Å0.290.59Cytokinin dehydrogenase 1
1diq.1.A14.81hetero-oligomerHHblitsX-ray2.75Å0.270.61P-CRESOL METHYLHYDROXYLASE
3s1f.1.A18.48monomerHHblitsX-ray2.00Å0.290.59Cytokinin dehydrogenase 1
2qpm.1.A18.48monomerHHblitsX-ray1.85Å0.290.59Cytokinin dehydrogenase 1
3kjm.1.A18.48monomerHHblitsX-ray1.90Å0.290.59Cytokinin dehydrogenase 1
1wve.1.A14.81hetero-oligomerHHblitsX-ray1.85Å0.270.614-cresol dehydrogenase [hydroxylating] flavoprotein subunit
3s1e.1.A18.48monomerHHblitsX-ray1.90Å0.290.59Cytokinin dehydrogenase 1
3s1d.1.A18.48monomerHHblitsX-ray1.75Å0.290.59Cytokinin dehydrogenase 1
5fxd.1.A14.81homo-dimerHHblitsX-ray1.70Å0.270.61PROBABLE VANILLYL-ALCOHOL OXIDASE
4bca.1.A13.89homo-dimerHHblitsX-ray2.40Å0.280.58ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
3rj8.1.A11.48monomerHHblitsX-ray2.40Å0.260.59Carbohydrate oxidase
4f4q.1.A18.13monomerHHblitsX-ray2.62Å0.290.55DprE1
4aut.1.A18.13monomerHHblitsX-ray2.10Å0.290.55DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE
4fdp.1.A19.88monomerHHblitsX-ray2.23Å0.290.53oxidoreductase DprE1
4fdp.2.A19.88monomerHHblitsX-ray2.23Å0.290.53oxidoreductase DprE1
4ncr.1.A19.88monomerHHblitsX-ray1.88Å0.290.53decaprenylphosphoryl-beta-D-ribose oxidase
3hsu.1.A17.58monomerHHblitsX-ray1.69Å0.290.53Glucooligosaccharide oxidase
2axr.1.A17.58monomerHHblitsX-ray1.98Å0.290.53glucooligosaccharide oxidase
4p8c.1.A20.12monomerHHblitsX-ray1.95Å0.290.53Probable decaprenylphosphoryl-beta-D-ribose oxidase
4p8c.2.A20.12monomerHHblitsX-ray1.95Å0.290.53Probable decaprenylphosphoryl-beta-D-ribose oxidase
4p8m.1.A20.12monomerHHblitsX-ray2.09Å0.290.53Probable decaprenylphosphoryl-beta-D-ribose oxidase
4xlo.1.A20.73homo-dimerHHblitsX-ray1.67Å0.290.53FAD-dependent oxygenase EncM
3w8w.1.A20.73homo-dimerHHblitsX-ray1.95Å0.290.53Putative FAD-dependent oxygenase EncM
4kw5.1.A20.25monomerHHblitsX-ray2.61Å0.290.52Oxidoreductase
1i19.1.A18.52monomerHHblitsX-ray1.70Å0.290.52CHOLESTEROL OXIDASE
2i0k.1.A18.75monomerHHblitsX-ray1.60Å0.300.51Oxidoreductase
2bvg.1.A19.02monomerHHblitsX-ray3.18Å0.280.526-HYDROXY-D-NICOTINE OXIDASE
3tsh.1.A20.37monomerHHblitsX-ray1.90Å0.290.52Pollen allergen Phl p 4
4pvj.1.A20.37monomerHHblitsX-ray1.80Å0.290.52Pollen allergen Phl p 4.0202
3fw7.1.A16.67monomerHHblitsX-ray1.82Å0.280.52Reticuline oxidase
2vfs.1.A18.24monomerHHblitsX-ray1.60Å0.300.51XYLITOL OXIDASE
3fw9.1.A16.67monomerHHblitsX-ray1.49Å0.280.52Reticuline oxidase
3js8.1.A14.81monomerHHblitsX-ray1.54Å0.280.52Cholesterol oxidase
3fw8.1.A16.05monomerHHblitsX-ray1.50Å0.280.52Reticuline oxidase
4pvk.1.A19.88monomerHHblitsX-ray1.30Å0.290.52Pollen allergen Phl p 4.0202
4pve.1.A19.88monomerHHblitsX-ray1.50Å0.290.52Pollen allergen Phl p 4.0202
4pvh.1.A19.88monomerHHblitsX-ray1.40Å0.290.52Pollen allergen Phl p 4.0202
4ec3.1.A16.15monomerHHblitsX-ray2.65Å0.280.52Reticuline oxidase
3d2j.1.A15.53monomerHHblitsX-ray2.05Å0.280.52berberine bridge-forming enzyme
3fwa.1.A15.53monomerHHblitsX-ray1.50Å0.280.52Reticuline oxidase
4dns.1.A16.77monomerHHblitsX-ray2.15Å0.280.52FAD-linked oxidoreductase BG60
4ud8.1.A15.53monomerHHblitsX-ray2.09Å0.280.52FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
4ud8.2.A15.53monomerHHblitsX-ray2.09Å0.280.52FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
5k8e.1.A17.50monomerHHblitsX-ray1.93Å0.280.51FAD linked oxidase-like protein
3gsy.1.A15.53monomerHHblitsX-ray1.63Å0.280.52Reticuline oxidase; Berberine bridge-forming enzyme
2wdw.1.A13.66homo-dimerHHblitsX-ray3.21Å0.280.52PUTATIVE HEXOSE OXIDASE
5awv.1.C13.66homo-tetramerHHblitsX-ray1.93Å0.280.52Putative hexose oxidase
3vte.1.A17.39monomerHHblitsX-ray2.75Å0.280.52Tetrahydrocannabinolic acid synthase
4pzf.1.A14.91monomerHHblitsX-ray2.20Å0.280.52Reticuline oxidase
2y3r.1.A15.53homo-dimerHHblitsX-ray1.79Å0.280.52TAML
5d79.1.A16.15monomerHHblitsX-ray1.85Å0.270.52Berberine bridge enzyme-like protein
2ipi.1.A18.35monomerHHblitsX-ray1.65Å0.290.51Aclacinomycin oxidoreductase (AknOx)
3pqb.1.A17.50homo-dimerHHblitsX-ray2.32Å0.270.51Putative oxidoreductase
5i1v.1.A13.04homo-dimerHHblitsX-ray1.84Å0.260.52CrmK
3b9j.1.B13.84hetero-oligomerHHblitsX-ray2.30Å0.270.51xanthine oxidase
3sr6.1.B13.92hetero-oligomerHHblitsX-ray2.10Å0.270.51Xanthine dehydrogenase/oxidase
1fiq.1.B13.92hetero-oligomerHHblitsX-ray2.50Å0.270.51XANTHINE OXIDASE
3nvv.1.B14.01hetero-oligomerHHblitsX-ray1.82Å0.270.50Xanthine dehydrogenase/oxidase
4uhw.1.A13.55homo-dimerHHblitsX-ray2.60Å0.270.50ALDEHYDE OXIDASE
5epg.1.A13.55homo-dimerHHblitsX-ray3.39Å0.270.50Aldehyde oxidase
3hrd.1.C17.22hetero-oligomerHHblitsX-ray2.20Å0.290.49Nicotinate dehydrogenase FAD-subunit
3amz.1.A12.26homo-dimerHHblitsX-ray2.10Å0.270.50Xanthine dehydrogenase/oxidase
3ax7.1.A12.26homo-dimerHHblitsX-ray2.34Å0.270.50Xanthine dehydrogenase/oxidase
4ytz.1.A12.26homo-dimerHHblitsX-ray2.30Å0.270.50Xanthine dehydrogenase/oxidase
4ytz.1.B12.26homo-dimerHHblitsX-ray2.30Å0.270.50Xanthine dehydrogenase/oxidase
4ysw.1.B12.26homo-dimerHHblitsX-ray1.99Å0.270.50Xanthine dehydrogenase/oxidase
3an1.1.A12.99homo-dimerHHblitsX-ray1.73Å0.270.50Xanthine dehydrogenase/oxidase
1wyg.1.A12.99monomerHHblitsX-ray2.60Å0.270.50Xanthine dehydrogenase/oxidase
2e3t.1.A12.99homo-dimerHHblitsX-ray2.28Å0.270.50Xanthine dehydrogenase/oxidase
2e3t.1.B12.99homo-dimerHHblitsX-ray2.28Å0.270.50Xanthine dehydrogenase/oxidase
1n5x.1.A12.99homo-dimerHHblitsX-ray2.80Å0.270.50Xanthine Dehydrogenase
3uni.1.A12.34homo-dimerHHblitsX-ray2.20Å0.270.50Xanthine dehydrogenase/oxidase
2ckj.1.A12.34homo-dimerHHblitsX-ray3.59Å0.270.50XANTHINE OXIDOREDUCTASE
2e1q.1.A12.34homo-dimerHHblitsX-ray2.60Å0.270.50Xanthine dehydrogenase/oxidase
3zyv.1.A10.32homo-dimerHHblitsX-ray2.55Å0.260.50AOX3
1zxi.1.C15.23hetero-oligomerHHblitsX-ray1.70Å0.280.49Carbon monoxide dehydrogenase medium chain
1ffv.1.C16.56hetero-oligomerHHblitsX-ray2.25Å0.280.49CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
1ffu.1.C17.33hetero-oligomerHHblitsX-ray2.35Å0.280.48CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
1n62.1.C16.00hetero-oligomerHHblitsX-ray1.09Å0.270.48Carbon monoxide dehydrogenase medium chain
1sb3.1.B14.77hetero-oligomerHHblitsX-ray2.20Å0.280.484-hydroxybenzoyl-CoA reductase beta subunit
1t3q.1.C10.07hetero-oligomerHHblitsX-ray1.80Å0.270.48quinoline 2-oxidoreductase medium subunit
2w3r.1.A10.74hetero-oligomerHHblitsX-ray2.90Å0.260.48XANTHINE DEHYDROGENASE
1jro.1.A10.74hetero-oligomerHHblitsX-ray2.70Å0.260.48xanthine dehydrogenase, chain A
4zoh.1.B12.24hetero-oligomerHHblitsX-ray2.20Å0.260.47Putative oxidoreductase FAD-binding subunit
4g3t.1.A25.89monomerHHblitsX-ray2.35Å0.330.36oxidoreductase DprE1
2yvs.1.A17.71homo-dimerHHblitsX-ray2.00Å0.280.31Glycolate oxidase subunit GlcE
2yvs.1.B17.71homo-dimerHHblitsX-ray2.00Å0.280.31Glycolate oxidase subunit GlcE
5d88.1.A15.29homo-dimerHHblitsX-ray1.66Å0.270.27Predicted protease of the collagenase family
3on1.1.A16.67monomerHHblitsX-ray1.65Å0.290.19BH2414 protein
1wn2.1.A13.16homo-dimerHHblitsX-ray1.20Å0.270.12Peptidyl-tRNA hydrolase
2d3k.1.A13.16homo-dimerHHblitsX-ray1.90Å0.270.12Peptidyl-tRNA hydrolase
2zv3.1.A16.22homo-dimerHHblitsX-ray2.10Å0.280.12Peptidyl-tRNA hydrolase
2zv3.3.B16.22homo-dimerHHblitsX-ray2.10Å0.280.12Peptidyl-tRNA hydrolase
2zv3.4.A16.22homo-dimerHHblitsX-ray2.10Å0.280.12Peptidyl-tRNA hydrolase
2zv3.4.B16.22homo-dimerHHblitsX-ray2.10Å0.280.12Peptidyl-tRNA hydrolase
1xty.1.A8.11homo-dimerHHblitsX-ray1.80Å0.270.12Peptidyl-tRNA hydrolase
1rlk.1.A10.81monomerHHblitsX-ray1.95Å0.250.12Hypothetical protein Ta0108
1q7s.1.A8.33monomerHHblitsX-ray2.00Å0.260.12bit1
1q7s.2.A8.33monomerHHblitsX-ray2.00Å0.260.12bit1
3erj.1.A16.67homo-dimerHHblitsX-ray1.80Å0.240.12Peptidyl-tRNA hydrolase
3erj.1.B16.67homo-dimerHHblitsX-ray1.80Å0.240.12Peptidyl-tRNA hydrolase
1rzw.1.A16.67monomerHHblitsNMRNA0.240.12Protein AF2095(GR4)
2epk.1.A14.29homo-dimerHHblitsX-ray1.85Å0.260.11N-acetyl-beta-D-glucosaminidase
2epo.1.A14.29homo-dimerHHblitsX-ray1.56Å0.260.11N-acetyl-beta-D-glucosaminidase