 |  | SWISS-MODEL Homology Modelling Report |
Model Building Report
This document lists the results for the homology modelling project "T5D7W9-MurB-H-pylori" submitted to SWISS-MODEL workspace on Oct. 17, 2017, 3:39 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 149 templates were found (Table T2).
Models
The following model was built (see Materials and Methods "Model Building"):
Model #01 | File | Built with | Oligo-State | Ligands | GMQE | QMEAN |
|---|---|---|---|---|---|---|
 | PDB | ProMod3 Version 1.0.2. | MONOMER | None | 0.69 | -3.41 |
|  |  |
| Template | Seq Identity | Oligo-state | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description |
|---|---|---|---|---|---|---|---|---|---|
| 4pyt.1.A | 30.08 | monomer | HHblits | X-ray | 1.85Å | 0.36 | 4 - 259 | 0.99 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| Ligand | Added to Model | Description |
|---|---|---|
| CL | ✕ - Not biologically relevant. | CHLORIDE ION |
| CL | ✕ - Not biologically relevant. | CHLORIDE ION |
| FAD | ✕ - Binding site not conserved. | FLAVIN-ADENINE DINUCLEOTIDE |
| MG | ✕ - Not biologically relevant. | MAGNESIUM ION |
| MG | ✕ - Not biologically relevant. | MAGNESIUM ION |
| MG | ✕ - Not biologically relevant. | MAGNESIUM ION |
Target MLETIIDFSRYSSVKIGVPLKVSVLENDDEI-----------SQEHQIIGLANNLLIAPG-AKNLALLG-KNYDYICDKG
4pyt.1.A ---ENEPLANHTTIKIGGPADCLVIPKDIQAVRDTMEVVKNHGVQWRAIGRGSNLLVLDEGIRGVVIKLGAGLDHMEIDG
Target ECIEIGGAANSSKIFNYFRANDLGGLEFLGQLPGTLGALVKMNAGMKEFEIKNVLESACI-----NNQWLGSGALGLDYR
4pyt.1.A EQVTVGGGYSVVRLSTGISKKGLSGLEFASGIPGSVGGAVYMNAGAHGSDISRILVKALILFEDGTMEWLTNEEMEFSYR
Target SSKFKG----VVLRARFKKTLGFREGV---LKACKSMRK-SHP-KLPNFGSCFKNPPNDYAGRLLEGVGLRGYCLKRVGF
4pyt.1.A TSILQNKRPGICLEAVLQLEQKERDAIVAQMQKNKDYRKETQPVSNPCAGSIFRNPLPDHAGRLVEQAGLKGHRIGGAKV
Target AKEHANFLVNLGGAEFEEALDLIELAKTRVLQEYGIHLEEEVKILR
4pyt.1.A SEMHGNFIVNAGGATAKDVLDLIAFIQKTIKEKYDIDMHTEVEIVG
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 8 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 141 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.
GTLGALVKMNAGMKEFEIKNVLESACINNQWLGSGALGLDYRSSKFKGVVLRARFKKTLGFREGVLKACKSMRKSHPKLPNFGSCFKNPPNDYAGRLLEG
VGLRGYCLKRVGFAKEHANFLVNLGGAEFEEALDLIELAKTRVLQEYGIHLEEEVKILR
Table T2:
| Template | Seq Identity | Oligo-state | Found by | Method | Resolution | Seq Similarity | Coverage | Description |
|---|---|---|---|---|---|---|---|---|
| 4pyt.1.A | 30.08 | monomer | HHblits | X-ray | 1.85Å | 0.36 | 0.99 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 4pyt.1.A | 32.27 | monomer | BLAST | X-ray | 1.85Å | 0.37 | 0.97 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 3tx1.1.A | 33.33 | monomer | BLAST | X-ray | 2.69Å | 0.36 | 0.96 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 3tx1.1.A | 30.20 | monomer | HHblits | X-ray | 2.69Å | 0.34 | 0.98 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 1hsk.1.A | 28.13 | monomer | HHblits | X-ray | 2.30Å | 0.34 | 0.99 | UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE |
| 4jay.1.A | 27.73 | monomer | HHblits | X-ray | 2.23Å | 0.32 | 0.99 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 4jb1.1.A | 27.73 | monomer | HHblits | X-ray | 2.10Å | 0.32 | 0.99 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 3i99.1.A | 24.90 | monomer | HHblits | X-ray | 2.20Å | 0.31 | 0.99 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 5jzx.1.A | 23.74 | homo-dimer | HHblits | X-ray | 2.20Å | 0.31 | 0.99 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 5jzx.1.B | 23.74 | homo-dimer | HHblits | X-ray | 2.20Å | 0.31 | 0.99 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 2mbr.1.A | 23.32 | monomer | HHblits | X-ray | 1.80Å | 0.32 | 0.98 | URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE |
| 1uxy.1.A | 22.92 | monomer | HHblits | X-ray | 1.80Å | 0.32 | 0.98 | URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE |
| 1mbb.1.A | 22.44 | monomer | HHblits | X-ray | 2.30Å | 0.31 | 0.98 | URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE |
| 1mbt.1.A | 22.44 | monomer | HHblits | X-ray | 3.00Å | 0.31 | 0.98 | URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE |
| 2q85.1.A | 22.44 | monomer | HHblits | X-ray | 2.51Å | 0.31 | 0.98 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 2gqu.1.A | 27.13 | monomer | HHblits | X-ray | 1.60Å | 0.33 | 0.95 | UDP-N-Acetylenolpyruvylglucosamine Reductase |
| 2gqt.1.A | 27.13 | monomer | HHblits | X-ray | 1.30Å | 0.33 | 0.95 | UDP-N-Acetylenolpyruvylglucosamine Reductase |
| 1hsk.1.A | 32.13 | monomer | BLAST | X-ray | 2.30Å | 0.36 | 0.85 | UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE |
| 4jay.1.A | 32.26 | monomer | BLAST | X-ray | 2.23Å | 0.34 | 0.84 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 4jb1.1.A | 32.26 | monomer | BLAST | X-ray | 2.10Å | 0.34 | 0.84 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 2gqu.1.A | 34.98 | monomer | BLAST | X-ray | 1.60Å | 0.38 | 0.78 | UDP-N-Acetylenolpyruvylglucosamine Reductase |
| 2gqt.1.A | 34.98 | monomer | BLAST | X-ray | 1.30Å | 0.38 | 0.78 | UDP-N-Acetylenolpyruvylglucosamine Reductase |
| 3i99.1.A | 35.33 | monomer | BLAST | X-ray | 2.20Å | 0.37 | 0.71 | UDP-N-acetylenolpyruvoylglucosamine reductase |
| 4f4q.1.A | 16.67 | monomer | HHblits | X-ray | 2.62Å | 0.28 | 0.58 | DprE1 |
| 4aut.1.A | 16.67 | monomer | HHblits | X-ray | 2.10Å | 0.28 | 0.58 | DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE |
| 3pm9.1.A | 14.84 | homo-dimer | HHblits | X-ray | 2.57Å | 0.25 | 0.60 | Putative oxidoreductase |
| 2vfs.1.A | 15.17 | monomer | HHblits | X-ray | 1.60Å | 0.28 | 0.56 | XYLITOL OXIDASE |
| 4fdp.1.A | 15.28 | monomer | HHblits | X-ray | 2.23Å | 0.27 | 0.56 | oxidoreductase DprE1 |
| 4fdp.2.A | 15.28 | monomer | HHblits | X-ray | 2.23Å | 0.27 | 0.56 | oxidoreductase DprE1 |
| 4ncr.1.A | 15.28 | monomer | HHblits | X-ray | 1.88Å | 0.27 | 0.56 | decaprenylphosphoryl-beta-D-ribose oxidase |
| 1w1k.1.A | 14.97 | homo-dimer | HHblits | X-ray | 2.55Å | 0.25 | 0.57 | VANILLYL-ALCOHOL OXIDASE |
| 5mxu.1.A | 14.97 | homo-octamer | HHblits | X-ray | 2.80Å | 0.25 | 0.57 | Vanillyl-alcohol oxidase |
| 4p8c.1.A | 15.28 | monomer | HHblits | X-ray | 1.95Å | 0.27 | 0.56 | Probable decaprenylphosphoryl-beta-D-ribose oxidase |
| 4p8c.2.A | 15.28 | monomer | HHblits | X-ray | 1.95Å | 0.27 | 0.56 | Probable decaprenylphosphoryl-beta-D-ribose oxidase |
| 4p8m.1.A | 15.28 | monomer | HHblits | X-ray | 2.09Å | 0.27 | 0.56 | Probable decaprenylphosphoryl-beta-D-ribose oxidase |
| 1w1m.1.A | 14.97 | homo-dimer | HHblits | X-ray | 3.00Å | 0.25 | 0.57 | VANILLYL-ALCOHOL OXIDASE |
| 1i19.1.A | 13.10 | monomer | HHblits | X-ray | 1.70Å | 0.26 | 0.56 | CHOLESTEROL OXIDASE |
| 1ahv.1.A | 14.29 | homo-octamer | HHblits | X-ray | 3.10Å | 0.25 | 0.57 | VANILLYL-ALCOHOL OXIDASE |
| 1ahu.1.A | 14.29 | homo-octamer | HHblits | X-ray | 2.70Å | 0.25 | 0.57 | VANILLYL-ALCOHOL OXIDASE |
| 4kw5.1.A | 15.38 | monomer | HHblits | X-ray | 2.61Å | 0.27 | 0.55 | Oxidoreductase |
| 2uuu.1.A | 11.56 | homo-dimer | HHblits | X-ray | 1.95Å | 0.25 | 0.57 | ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE |
| 2uuv.2.B | 11.56 | homo-dimer | HHblits | X-ray | 1.99Å | 0.25 | 0.57 | ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE |
| 1e8g.1.A | 14.38 | homo-octamer | HHblits | X-ray | 2.10Å | 0.25 | 0.56 | VANILLYL-ALCOHOL OXIDASE |
| 3js8.1.A | 11.72 | monomer | HHblits | X-ray | 1.54Å | 0.26 | 0.56 | Cholesterol oxidase |
| 1dzn.1.A | 13.61 | homo-octamer | HHblits | X-ray | 2.80Å | 0.25 | 0.57 | VANILLYL-ALCOHOL OXIDASE |
| 1w1j.1.A | 14.38 | homo-dimer | HHblits | X-ray | 2.70Å | 0.25 | 0.56 | VANILLYL-ALCOHOL OXIDASE |
| 3b9j.1.B | 8.16 | hetero-oligomer | HHblits | X-ray | 2.30Å | 0.24 | 0.57 | xanthine oxidase |
| 1fiq.1.B | 8.16 | hetero-oligomer | HHblits | X-ray | 2.50Å | 0.24 | 0.57 | XANTHINE OXIDASE |
| 2axr.1.A | 11.56 | monomer | HHblits | X-ray | 1.98Å | 0.24 | 0.57 | glucooligosaccharide oxidase |
| 4ml8.1.A | 9.52 | monomer | HHblits | X-ray | 2.70Å | 0.24 | 0.57 | Cytokinin oxidase 2 |
| 3hsu.1.A | 11.64 | monomer | HHblits | X-ray | 1.69Å | 0.24 | 0.56 | Glucooligosaccharide oxidase |
| 3nvv.1.B | 8.22 | hetero-oligomer | HHblits | X-ray | 1.82Å | 0.24 | 0.56 | Xanthine dehydrogenase/oxidase |
| 2e3t.1.A | 8.28 | homo-dimer | HHblits | X-ray | 2.28Å | 0.25 | 0.56 | Xanthine dehydrogenase/oxidase |
| 2e3t.1.B | 8.28 | homo-dimer | HHblits | X-ray | 2.28Å | 0.25 | 0.56 | Xanthine dehydrogenase/oxidase |
| 1wyg.1.A | 7.59 | monomer | HHblits | X-ray | 2.60Å | 0.25 | 0.56 | Xanthine dehydrogenase/oxidase |
| 4ytz.1.A | 7.59 | homo-dimer | HHblits | X-ray | 2.30Å | 0.25 | 0.56 | Xanthine dehydrogenase/oxidase |
| 4ytz.1.B | 7.59 | homo-dimer | HHblits | X-ray | 2.30Å | 0.25 | 0.56 | Xanthine dehydrogenase/oxidase |
| 4ysw.1.B | 7.59 | homo-dimer | HHblits | X-ray | 1.99Å | 0.25 | 0.56 | Xanthine dehydrogenase/oxidase |
| 4o95.1.A | 8.90 | monomer | HHblits | X-ray | 1.75Å | 0.24 | 0.56 | Cytokinin dehydrogenase 4 |
| 5hhz.1.A | 8.90 | monomer | HHblits | X-ray | 2.00Å | 0.24 | 0.56 | Cytokinin dehydrogenase 4 |
| 5epg.1.A | 7.53 | homo-dimer | HHblits | X-ray | 3.39Å | 0.24 | 0.56 | Aldehyde oxidase |
| 2i0k.1.A | 11.89 | monomer | HHblits | X-ray | 1.60Å | 0.26 | 0.55 | Oxidoreductase |
| 4bc7.1.A | 11.11 | homo-dimer | HHblits | X-ray | 2.40Å | 0.25 | 0.56 | ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL |
| 4bby.1.A | 11.11 | homo-dimer | HHblits | X-ray | 1.90Å | 0.25 | 0.56 | ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL |
| 3sr6.1.B | 8.28 | hetero-oligomer | HHblits | X-ray | 2.10Å | 0.24 | 0.56 | Xanthine dehydrogenase/oxidase |
| 5fxd.1.A | 10.34 | homo-dimer | HHblits | X-ray | 1.70Å | 0.24 | 0.56 | PROBABLE VANILLYL-ALCOHOL OXIDASE |
| 3uni.1.A | 8.33 | homo-dimer | HHblits | X-ray | 2.20Å | 0.24 | 0.56 | Xanthine dehydrogenase/oxidase |
| 4bca.1.A | 11.19 | homo-dimer | HHblits | X-ray | 2.40Å | 0.25 | 0.55 | ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL |
| 2ckj.1.A | 6.21 | homo-dimer | HHblits | X-ray | 3.59Å | 0.24 | 0.56 | XANTHINE OXIDOREDUCTASE |
| 5k8e.1.A | 11.03 | monomer | HHblits | X-ray | 1.93Å | 0.24 | 0.56 | FAD linked oxidase-like protein |
| 2e1q.1.A | 6.21 | homo-dimer | HHblits | X-ray | 2.60Å | 0.24 | 0.56 | Xanthine dehydrogenase/oxidase |
| 3pqb.1.A | 14.18 | homo-dimer | HHblits | X-ray | 2.32Å | 0.26 | 0.54 | Putative oxidoreductase |
| 4uhw.1.A | 6.90 | homo-dimer | HHblits | X-ray | 2.60Å | 0.24 | 0.56 | ALDEHYDE OXIDASE |
| 2bvg.1.A | 13.89 | monomer | HHblits | X-ray | 3.18Å | 0.24 | 0.56 | 6-HYDROXY-D-NICOTINE OXIDASE |
| 1diq.1.A | 11.03 | hetero-oligomer | HHblits | X-ray | 2.75Å | 0.23 | 0.56 | P-CRESOL METHYLHYDROXYLASE |
| 3w8w.1.A | 13.79 | homo-dimer | HHblits | X-ray | 1.95Å | 0.23 | 0.56 | Putative FAD-dependent oxygenase EncM |
| 1w1q.1.A | 10.49 | monomer | HHblits | X-ray | 1.80Å | 0.24 | 0.55 | CYTOKININ DEHYDROGENASE 1 |
| 3s1d.1.A | 10.49 | monomer | HHblits | X-ray | 1.75Å | 0.24 | 0.55 | Cytokinin dehydrogenase 1 |
| 3vte.1.A | 10.49 | monomer | HHblits | X-ray | 2.75Å | 0.24 | 0.55 | Tetrahydrocannabinolic acid synthase |
| 4xlo.1.A | 13.10 | homo-dimer | HHblits | X-ray | 1.67Å | 0.23 | 0.56 | FAD-dependent oxygenase EncM |
| 3s1f.1.A | 10.56 | monomer | HHblits | X-ray | 2.00Å | 0.24 | 0.55 | Cytokinin dehydrogenase 1 |
| 3s1e.1.A | 10.56 | monomer | HHblits | X-ray | 1.90Å | 0.24 | 0.55 | Cytokinin dehydrogenase 1 |
| 3fwa.1.A | 9.86 | monomer | HHblits | X-ray | 1.50Å | 0.24 | 0.55 | Reticuline oxidase |
| 1wve.1.A | 10.42 | hetero-oligomer | HHblits | X-ray | 1.85Å | 0.23 | 0.56 | 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit |
| 4pzf.1.A | 9.86 | monomer | HHblits | X-ray | 2.20Å | 0.24 | 0.55 | Reticuline oxidase |
| 2w3r.1.A | 14.49 | hetero-oligomer | HHblits | X-ray | 2.90Å | 0.26 | 0.53 | XANTHINE DEHYDROGENASE |
| 2q4w.1.A | 10.49 | monomer | HHblits | X-ray | 1.70Å | 0.23 | 0.55 | Cytokinin dehydrogenase 7 |
| 1jro.1.A | 14.49 | hetero-oligomer | HHblits | X-ray | 2.70Å | 0.26 | 0.53 | xanthine dehydrogenase, chain A |
| 3fw9.1.A | 9.15 | monomer | HHblits | X-ray | 1.49Å | 0.24 | 0.55 | Reticuline oxidase |
| 3d2j.1.A | 9.93 | monomer | HHblits | X-ray | 2.05Å | 0.24 | 0.54 | berberine bridge-forming enzyme |
| 3rj8.1.A | 6.21 | monomer | HHblits | X-ray | 2.40Å | 0.22 | 0.56 | Carbohydrate oxidase |
| 3fw8.1.A | 9.93 | monomer | HHblits | X-ray | 1.50Å | 0.24 | 0.54 | Reticuline oxidase |
| 3gsy.1.A | 9.93 | monomer | HHblits | X-ray | 1.63Å | 0.24 | 0.54 | Reticuline oxidase; Berberine bridge-forming enzyme |
| 2qpm.1.A | 10.64 | monomer | HHblits | X-ray | 1.85Å | 0.24 | 0.54 | Cytokinin dehydrogenase 1 |
| 3kjm.1.A | 10.64 | monomer | HHblits | X-ray | 1.90Å | 0.24 | 0.54 | Cytokinin dehydrogenase 1 |
| 3dq0.1.A | 10.64 | monomer | HHblits | X-ray | 1.90Å | 0.24 | 0.54 | Cytokinin dehydrogenase 1 |
| 4ec3.1.A | 9.93 | monomer | HHblits | X-ray | 2.65Å | 0.24 | 0.54 | Reticuline oxidase |
| 4pve.1.A | 7.69 | monomer | HHblits | X-ray | 1.50Å | 0.23 | 0.55 | Pollen allergen Phl p 4.0202 |
| 4pvk.1.A | 7.69 | monomer | HHblits | X-ray | 1.30Å | 0.23 | 0.55 | Pollen allergen Phl p 4.0202 |
| 3fw7.1.A | 9.93 | monomer | HHblits | X-ray | 1.82Å | 0.24 | 0.54 | Reticuline oxidase |
| 3tsh.1.A | 8.45 | monomer | HHblits | X-ray | 1.90Å | 0.23 | 0.55 | Pollen allergen Phl p 4 |
| 4dns.1.A | 8.39 | monomer | HHblits | X-ray | 2.15Å | 0.23 | 0.55 | FAD-linked oxidoreductase BG60 |
| 4pvh.1.A | 7.75 | monomer | HHblits | X-ray | 1.40Å | 0.23 | 0.55 | Pollen allergen Phl p 4.0202 |
| 4pvj.1.A | 7.80 | monomer | HHblits | X-ray | 1.80Å | 0.23 | 0.54 | Pollen allergen Phl p 4.0202 |
| 5d79.1.A | 9.15 | monomer | HHblits | X-ray | 1.85Å | 0.22 | 0.55 | Berberine bridge enzyme-like protein |
| 5i1v.1.A | 8.63 | homo-dimer | HHblits | X-ray | 1.84Å | 0.24 | 0.54 | CrmK |
| 2ipi.1.A | 8.63 | monomer | HHblits | X-ray | 1.65Å | 0.24 | 0.54 | Aclacinomycin oxidoreductase (AknOx) |
| 2y3r.1.A | 8.63 | homo-dimer | HHblits | X-ray | 1.79Å | 0.24 | 0.54 | TAML |
| 4ud8.1.A | 7.75 | monomer | HHblits | X-ray | 2.09Å | 0.22 | 0.55 | FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN |
| 4ud8.2.A | 7.75 | monomer | HHblits | X-ray | 2.09Å | 0.22 | 0.55 | FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN |
| 2wdw.1.A | 8.63 | homo-dimer | HHblits | X-ray | 3.21Å | 0.23 | 0.54 | PUTATIVE HEXOSE OXIDASE |
| 5awv.1.C | 8.63 | homo-tetramer | HHblits | X-ray | 1.93Å | 0.23 | 0.54 | Putative hexose oxidase |
| 4zoh.1.B | 13.64 | hetero-oligomer | HHblits | X-ray | 2.20Å | 0.26 | 0.51 | Putative oxidoreductase FAD-binding subunit |
| 1ffu.1.C | 10.61 | hetero-oligomer | HHblits | X-ray | 2.35Å | 0.24 | 0.51 | CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE |
| 3hrd.1.C | 13.01 | hetero-oligomer | HHblits | X-ray | 2.20Å | 0.27 | 0.47 | Nicotinate dehydrogenase FAD-subunit |
| 1n62.1.C | 8.94 | hetero-oligomer | HHblits | X-ray | 1.09Å | 0.24 | 0.47 | Carbon monoxide dehydrogenase medium chain |
| 1zxi.1.C | 8.94 | hetero-oligomer | HHblits | X-ray | 1.70Å | 0.24 | 0.47 | Carbon monoxide dehydrogenase medium chain |
| 1ffv.1.C | 11.48 | hetero-oligomer | HHblits | X-ray | 2.25Å | 0.25 | 0.47 | CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE |
| 1t3q.1.C | 11.57 | hetero-oligomer | HHblits | X-ray | 1.80Å | 0.25 | 0.47 | quinoline 2-oxidoreductase medium subunit |
| 1qlt.1.A | 14.41 | homo-octamer | HHblits | X-ray | 2.20Å | 0.25 | 0.46 | VANILLYL-ALCOHOL OXIDASE |
| 5mxj.1.A | 13.56 | homo-octamer | HHblits | X-ray | 2.80Å | 0.25 | 0.46 | Vanillyl-alcohol oxidase |
| 1w1l.1.A | 12.82 | homo-dimer | HHblits | X-ray | 2.70Å | 0.24 | 0.45 | VANILLYL-ALCOHOL OXIDASE |
| 1e0y.1.A | 12.82 | homo-dimer | HHblits | X-ray | 2.75Å | 0.24 | 0.45 | VANILLYL-ALCOHOL OXIDASE |
| 4g3t.1.A | 17.76 | monomer | HHblits | X-ray | 2.35Å | 0.29 | 0.41 | oxidoreductase DprE1 |
| 1f0x.1.A | 6.93 | monomer | HHblits | X-ray | 1.90Å | 0.22 | 0.39 | D-LACTATE DEHYDROGENASE |
| 2yvs.1.A | 16.13 | homo-dimer | HHblits | X-ray | 2.00Å | 0.26 | 0.36 | Glycolate oxidase subunit GlcE |
| 2yvs.1.B | 16.13 | homo-dimer | HHblits | X-ray | 2.00Å | 0.26 | 0.36 | Glycolate oxidase subunit GlcE |
| 1m1b.1.A | 10.20 | homo-tetramer | HHblits | X-ray | 2.25Å | 0.29 | 0.19 | PHOSPHOENOLPYRUVATE PHOSPHOMUTASE |
| 1s2v.1.A | 10.20 | homo-tetramer | HHblits | X-ray | 2.10Å | 0.29 | 0.19 | Phosphoenolpyruvate phosphomutase |
| 1s2w.1.A | 10.20 | monomer | HHblits | X-ray | 1.69Å | 0.29 | 0.19 | Phosphoenolpyruvate phosphomutase |
| 2ze3.1.A | 20.41 | homo-dimer | HHblits | X-ray | 1.65Å | 0.28 | 0.19 | DFA0005 |
| 1s2u.1.A | 10.20 | homo-tetramer | HHblits | X-ray | 2.00Å | 0.28 | 0.19 | Phosphoenolpyruvate phosphomutase |
| 3m0k.1.A | 12.24 | homo-tetramer | HHblits | X-ray | 1.65Å | 0.27 | 0.19 | Oxaloacetate acetylhydrolase |
| 5unc.1.A | 18.37 | homo-tetramer | HHblits | X-ray | 1.71Å | 0.27 | 0.19 | PHOSPHOENOLPYRUVATE PHOSPHOMUTASE |
| 4iqd.1.A | 14.29 | homo-dimer | HHblits | X-ray | 2.00Å | 0.27 | 0.19 | Carboxyvinyl-carboxyphosphonate phosphorylmutase |
| 4iqe.1.B | 14.29 | homo-dimer | HHblits | X-ray | 2.50Å | 0.27 | 0.19 | Carboxyvinyl-carboxyphosphonate phosphorylmutase |
| 2hjp.1.A | 12.24 | homo-tetramer | HHblits | X-ray | 1.90Å | 0.27 | 0.19 | Phosphonopyruvate hydrolase |
| 1zlp.1.A | 10.42 | homo-tetramer | HHblits | X-ray | 2.70Å | 0.27 | 0.19 | petal death protein |
| 3n4w.1.B | 8.70 | homo-dimer | HHblits | X-ray | 1.45Å | 0.26 | 0.18 | Receptor-type tyrosine-protein phosphatase-like N |
| 3n4w.1.A | 8.70 | homo-dimer | HHblits | X-ray | 1.45Å | 0.26 | 0.18 | Receptor-type tyrosine-protein phosphatase-like N |
| 3np5.1.A | 8.70 | homo-tetramer | HHblits | X-ray | 1.80Å | 0.26 | 0.18 | Receptor-type tyrosine-protein phosphatase-like N |
| 3n01.1.A | 8.70 | homo-dimer | HHblits | X-ray | 1.30Å | 0.26 | 0.18 | Receptor-type tyrosine-protein phosphatase-like N |
| 3n01.1.B | 8.70 | homo-dimer | HHblits | X-ray | 1.30Å | 0.26 | 0.18 | Receptor-type tyrosine-protein phosphatase-like N |
| 3np5.1.B | 8.70 | homo-tetramer | HHblits | X-ray | 1.80Å | 0.26 | 0.18 | Receptor-type tyrosine-protein phosphatase-like N |
| 3np5.1.D | 8.70 | homo-tetramer | HHblits | X-ray | 1.80Å | 0.26 | 0.18 | Receptor-type tyrosine-protein phosphatase-like N |
| 2qt7.1.A | 8.89 | homo-tetramer | HHblits | X-ray | 1.30Å | 0.26 | 0.17 | Receptor-type tyrosine-protein phosphatase-like N |
| 2qt7.1.B | 8.89 | homo-tetramer | HHblits | X-ray | 1.30Å | 0.26 | 0.17 | Receptor-type tyrosine-protein phosphatase-like N |
| 4hti.1.A | 13.95 | monomer | HHblits | X-ray | 1.95Å | 0.27 | 0.17 | Receptor-type tyrosine-protein phosphatase N2 |
| 4htj.1.A | 13.95 | monomer | HHblits | X-ray | 2.01Å | 0.27 | 0.17 | Receptor-type tyrosine-protein phosphatase N2 |