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SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "R2PDM0-MurB-E-faecium" submitted to SWISS-MODEL workspace on Oct. 17, 2017, 3:46 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 164 templates were found (Table T2).

Models

The following models were 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	0.77	-0.54

QMEAN	-0.54
Cβ	0.87
All Atom	-0.44
Solvation	0.26
Torsion	-0.74

Template	Seq Identity	Oligo-state	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
3tx1.1.A	56.94	monomer	BLAST	X-ray	2.69Å	0.46	13 - 300	0.93	UDP-N-acetylenolpyruvoylglucosamine reductase

Ligand	Added to Model	Description
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    MNKEEIVESLATITLLFDEPLMNYTFTKTGGPADVLAFPKKQEEVKQIIDYCRIHDISWMVLGNASNLIVQDGGIRGVVI
3tx1.1.A  ------------IAIKLNEPLSKYTYTKTGGAADVFVMPKTIEEAQEVVAYCHQNKIPLTILGNGSNLIIKDGGIRGVIL

Target    MLTEMKQIHVKGTMVIAEAGASLIDTTYAALAESLTGFEFACGIPGSVGGAVYMNAGAYGGEIKDVFAEVDLLLEDGTLK
3tx1.1.A  HLDLLQTIERNNTQIVAMSGAKLIDTAKFALNESLSGLEFACGIPGSIGGALHMNAGAYGGEISDVLEAATVLTQTGELK

Target    TLTKEEMVFSYRHSKVQELRAIVLEARFSLQTGDYEAIKARMDELTELRQSKQPLEYPSCGSVFKRPVGHYTGQLIQQAG
3tx1.1.A  KLKRSELKAAYRFSTIAEKNYIVLDATFSLALEEKNLIQAKMDELTAAREAKQPLEYPSCGSVFKRPPGHFAGKLIQDSG

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

Model #02	File	Built with	Oligo-State	Ligands	GMQE	QMEAN
	PDB	ProMod3 Version 1.0.2.	MONOMER	None	0.46	-4.21

QMEAN	-4.21
Cβ	-2.12
All Atom	-2.77
Solvation	-1.12
Torsion	-3.40

Template	Seq Identity	Oligo-state	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
3i99.1.A	37.50	monomer	BLAST	X-ray	2.20Å	0.37	84 - 298	0.69	UDP-N-acetylenolpyruvoylglucosamine reductase

Ligand	Added to Model	Description
FAD	✕ - Binding site not conserved.	FLAVIN-ADENINE DINUCLEOTIDE
PO4	✕ - Not biologically relevant.	PHOSPHATE ION
PO4	✕ - Not biologically relevant.	PHOSPHATE ION

Target    MNKEEIVESLATITLLFDEPLMNYTFTKTGGPADVLAFPKKQEEVKQIIDYCRIHDISWMVLGNASNLIVQDGGIRGVVI
3i99.1.A  --------------------------------------------------------------------------------

Target    MLTEMKQIHVKGTMVIAEAGASLIDTTYAALAESLTGFEFACGIPGSVGGAVYMNAGAYGGEIKDVFAEVD-LLLEDGTL
3i99.1.A  ---DYHRLHVAG----GEDWPSLVSW---CVEQGIGGLENLALIPGCAGSAPIQNIGAYGVEFKDVCDYVEYLCLETGTV

Target    KTLTKEEMVFSYR-----HSKVQELRAIVLEARFS------LQTGDYE------AIKARMDELTELRQSK--QPLEYPSC
3i99.1.A  KRLTMEECQFGYRDSIFKHQLYQKAVVTAVGLKFAKAWQPIIQYGPLKDLSSDCAIHDVYQRVCATRMEKLPDPAVMGNA

Target    GSVFKRPV-------------GHYTGQLIQQAGLQGLKW------------GGAQISEKHAGFIVNIDHATATDYIELIA
3i99.1.A  GSFFKNPVISQQAFARLQIEHPDVVAYPAEQGVKVAAGWLIDQAGLKGHQIGGAKVHPKQALVIVNTGDASAQDVLMLAA

Target    HIQEVIKEKFDVSLETEVRIIGE------KQALSETSRSLAN
3i99.1.A  DIQQRVFNCYGIELEHEVRFIGESEETNLKQWMSEQA-----

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 149 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.

MNKEEIVESLATITLLFDEPLMNYTFTKTGGPADVLAFPKKQEEVKQIIDYCRIHDISWMVLGNASNLIVQDGGIRGVVIMLTEMKQIHVKGTMVIAEAG
ASLIDTTYAALAESLTGFEFACGIPGSVGGAVYMNAGAYGGEIKDVFAEVDLLLEDGTLKTLTKEEMVFSYRHSKVQELRAIVLEARFSLQTGDYEAIKA
RMDELTELRQSKQPLEYPSCGSVFKRPVGHYTGQLIQQAGLQGLKWGGAQISEKHAGFIVNIDHATATDYIELIAHIQEVIKEKFDVSLETEVRIIGEKQ
ALSETSRSLAN

Table T2:

Template	Seq Identity	Oligo-state	Found by	Method	Resolution	Seq Similarity	Coverage	Description
3tx1.1.A	55.59	monomer	HHblits	X-ray	2.69Å	0.45	0.95	UDP-N-acetylenolpyruvoylglucosamine reductase
1hsk.1.A	51.17	monomer	HHblits	X-ray	2.30Å	0.44	0.96	UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE
3tx1.1.A	56.94	monomer	BLAST	X-ray	2.69Å	0.46	0.93	UDP-N-acetylenolpyruvoylglucosamine reductase
1hsk.1.A	54.09	monomer	BLAST	X-ray	2.30Å	0.45	0.90	UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE
4pyt.1.A	44.90	monomer	BLAST	X-ray	1.85Å	0.42	0.95	UDP-N-acetylenolpyruvoylglucosamine reductase
4pyt.1.A	45.30	monomer	HHblits	X-ray	1.85Å	0.42	0.92	UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.A	28.87	homo-dimer	HHblits	X-ray	2.20Å	0.33	0.94	UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.B	28.87	homo-dimer	HHblits	X-ray	2.20Å	0.33	0.94	UDP-N-acetylenolpyruvoylglucosamine reductase
3i99.1.A	29.72	monomer	HHblits	X-ray	2.20Å	0.34	0.92	UDP-N-acetylenolpyruvoylglucosamine reductase
1mbb.1.A	28.62	monomer	HHblits	X-ray	2.30Å	0.34	0.91	URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1mbt.1.A	28.62	monomer	HHblits	X-ray	3.00Å	0.34	0.91	URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2q85.1.A	28.62	monomer	HHblits	X-ray	2.51Å	0.34	0.91	UDP-N-acetylenolpyruvoylglucosamine reductase
4jay.1.A	29.08	monomer	HHblits	X-ray	2.23Å	0.34	0.91	UDP-N-acetylenolpyruvoylglucosamine reductase
4jb1.1.A	29.08	monomer	HHblits	X-ray	2.10Å	0.34	0.91	UDP-N-acetylenolpyruvoylglucosamine reductase
1uxy.1.A	28.37	monomer	HHblits	X-ray	1.80Å	0.34	0.91	URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2mbr.1.A	28.83	monomer	HHblits	X-ray	1.80Å	0.34	0.90	URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2gqu.1.A	38.40	monomer	HHblits	X-ray	1.60Å	0.37	0.85	UDP-N-Acetylenolpyruvylglucosamine Reductase
2gqt.1.A	38.40	monomer	HHblits	X-ray	1.30Å	0.37	0.85	UDP-N-Acetylenolpyruvylglucosamine Reductase
4jay.1.A	30.38	monomer	BLAST	X-ray	2.23Å	0.34	0.84	UDP-N-acetylenolpyruvoylglucosamine reductase
4jb1.1.A	30.38	monomer	BLAST	X-ray	2.10Å	0.34	0.84	UDP-N-acetylenolpyruvoylglucosamine reductase
2gqu.1.A	40.16	monomer	BLAST	X-ray	1.60Å	0.38	0.78	UDP-N-Acetylenolpyruvylglucosamine Reductase
2gqt.1.A	40.16	monomer	BLAST	X-ray	1.30Å	0.38	0.78	UDP-N-Acetylenolpyruvylglucosamine Reductase
1mbb.1.A	34.89	monomer	BLAST	X-ray	2.30Å	0.36	0.76	URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1mbt.1.A	34.89	monomer	BLAST	X-ray	3.00Å	0.36	0.76	URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
2q85.1.A	34.89	monomer	BLAST	X-ray	2.51Å	0.36	0.76	UDP-N-acetylenolpyruvoylglucosamine reductase
2mbr.1.A	34.89	monomer	BLAST	X-ray	1.80Å	0.36	0.76	URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
1uxy.1.A	34.47	monomer	BLAST	X-ray	1.80Å	0.36	0.76	URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
5jzx.1.A	32.07	homo-dimer	BLAST	X-ray	2.20Å	0.35	0.76	UDP-N-acetylenolpyruvoylglucosamine reductase
5jzx.1.B	32.07	homo-dimer	BLAST	X-ray	2.20Å	0.35	0.76	UDP-N-acetylenolpyruvoylglucosamine reductase
3i99.1.A	37.50	monomer	BLAST	X-ray	2.20Å	0.37	0.69	UDP-N-acetylenolpyruvoylglucosamine reductase
2uuu.1.A	15.68	homo-dimer	HHblits	X-ray	1.95Å	0.29	0.59	ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE
2uuv.2.B	15.68	homo-dimer	HHblits	X-ray	1.99Å	0.29	0.59	ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE
4bc7.1.A	13.81	homo-dimer	HHblits	X-ray	2.40Å	0.28	0.58	ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
4bby.1.A	13.81	homo-dimer	HHblits	X-ray	1.90Å	0.28	0.58	ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
4bca.1.A	13.89	homo-dimer	HHblits	X-ray	2.40Å	0.28	0.58	ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
3pm9.1.A	21.59	homo-dimer	HHblits	X-ray	2.57Å	0.29	0.57	Putative oxidoreductase
3rj8.1.A	11.48	monomer	HHblits	X-ray	2.40Å	0.26	0.59	Carbohydrate oxidase
4ml8.1.A	14.20	monomer	HHblits	X-ray	2.70Å	0.29	0.57	Cytokinin oxidase 2
4f4q.1.A	19.30	monomer	HHblits	X-ray	2.62Å	0.29	0.55	DprE1
4aut.1.A	19.30	monomer	HHblits	X-ray	2.10Å	0.29	0.55	DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE
4kw5.1.A	20.96	monomer	HHblits	X-ray	2.61Å	0.30	0.54	Oxidoreductase
1e8g.1.A	17.47	homo-octamer	HHblits	X-ray	2.10Å	0.29	0.53	VANILLYL-ALCOHOL OXIDASE
2axr.1.A	18.18	monomer	HHblits	X-ray	1.98Å	0.29	0.53	glucooligosaccharide oxidase
1qlt.1.A	17.47	homo-octamer	HHblits	X-ray	2.20Å	0.28	0.53	VANILLYL-ALCOHOL OXIDASE
1dzn.1.A	16.87	homo-octamer	HHblits	X-ray	2.80Å	0.28	0.53	VANILLYL-ALCOHOL OXIDASE
1w1m.1.A	16.87	homo-dimer	HHblits	X-ray	3.00Å	0.28	0.53	VANILLYL-ALCOHOL OXIDASE
5mxu.1.A	16.87	homo-octamer	HHblits	X-ray	2.80Å	0.28	0.53	Vanillyl-alcohol oxidase
1w1k.1.A	16.87	homo-dimer	HHblits	X-ray	2.55Å	0.28	0.53	VANILLYL-ALCOHOL OXIDASE
1w1j.1.A	16.87	homo-dimer	HHblits	X-ray	2.70Å	0.28	0.53	VANILLYL-ALCOHOL OXIDASE
4xlo.1.A	20.73	homo-dimer	HHblits	X-ray	1.67Å	0.29	0.53	FAD-dependent oxygenase EncM
1ahv.1.A	16.87	homo-octamer	HHblits	X-ray	3.10Å	0.28	0.53	VANILLYL-ALCOHOL OXIDASE
1ahu.1.A	16.87	homo-octamer	HHblits	X-ray	2.70Å	0.28	0.53	VANILLYL-ALCOHOL OXIDASE
4p8c.1.A	20.99	monomer	HHblits	X-ray	1.95Å	0.30	0.52	Probable decaprenylphosphoryl-beta-D-ribose oxidase
4p8c.2.A	20.99	monomer	HHblits	X-ray	1.95Å	0.30	0.52	Probable decaprenylphosphoryl-beta-D-ribose oxidase
4p8m.1.A	20.99	monomer	HHblits	X-ray	2.09Å	0.30	0.52	Probable decaprenylphosphoryl-beta-D-ribose oxidase
1i19.1.A	18.40	monomer	HHblits	X-ray	1.70Å	0.29	0.52	CHOLESTEROL OXIDASE
3w8w.1.A	20.86	homo-dimer	HHblits	X-ray	1.95Å	0.29	0.52	Putative FAD-dependent oxygenase EncM
4fdp.1.A	21.12	monomer	HHblits	X-ray	2.23Å	0.30	0.52	oxidoreductase DprE1
4fdp.2.A	21.12	monomer	HHblits	X-ray	2.23Å	0.30	0.52	oxidoreductase DprE1
4ncr.1.A	21.12	monomer	HHblits	X-ray	1.88Å	0.30	0.52	decaprenylphosphoryl-beta-D-ribose oxidase
3hsu.1.A	17.07	monomer	HHblits	X-ray	1.69Å	0.28	0.53	Glucooligosaccharide oxidase
4o95.1.A	17.18	monomer	HHblits	X-ray	1.75Å	0.29	0.52	Cytokinin dehydrogenase 4
5hhz.1.A	17.18	monomer	HHblits	X-ray	2.00Å	0.29	0.52	Cytokinin dehydrogenase 4
2i0k.1.A	18.63	monomer	HHblits	X-ray	1.60Å	0.30	0.52	Oxidoreductase
5fxd.1.A	15.15	homo-dimer	HHblits	X-ray	1.70Å	0.28	0.53	PROBABLE VANILLYL-ALCOHOL OXIDASE
5k8e.1.A	17.79	monomer	HHblits	X-ray	1.93Å	0.28	0.52	FAD linked oxidase-like protein
2vfs.1.A	19.50	monomer	HHblits	X-ray	1.60Å	0.30	0.51	XYLITOL OXIDASE
3s1d.1.A	18.13	monomer	HHblits	X-ray	1.75Å	0.30	0.51	Cytokinin dehydrogenase 1
1w1q.1.A	18.13	monomer	HHblits	X-ray	1.80Å	0.30	0.51	CYTOKININ DEHYDROGENASE 1
2bvg.1.A	19.75	monomer	HHblits	X-ray	3.18Å	0.28	0.52	6-HYDROXY-D-NICOTINE OXIDASE
2q4w.1.A	18.52	monomer	HHblits	X-ray	1.70Å	0.28	0.52	Cytokinin dehydrogenase 7
2qpm.1.A	18.24	monomer	HHblits	X-ray	1.85Å	0.30	0.51	Cytokinin dehydrogenase 1
3kjm.1.A	18.24	monomer	HHblits	X-ray	1.90Å	0.30	0.51	Cytokinin dehydrogenase 1
3s1e.1.A	18.24	monomer	HHblits	X-ray	1.90Å	0.30	0.51	Cytokinin dehydrogenase 1
3dq0.1.A	18.24	monomer	HHblits	X-ray	1.90Å	0.30	0.51	Cytokinin dehydrogenase 1
3s1f.1.A	18.24	monomer	HHblits	X-ray	2.00Å	0.30	0.51	Cytokinin dehydrogenase 1
1diq.1.A	13.33	hetero-oligomer	HHblits	X-ray	2.75Å	0.27	0.53	P-CRESOL METHYLHYDROXYLASE
4pvk.1.A	18.52	monomer	HHblits	X-ray	1.30Å	0.28	0.52	Pollen allergen Phl p 4.0202
3fwa.1.A	16.67	monomer	HHblits	X-ray	1.50Å	0.28	0.52	Reticuline oxidase
4pve.1.A	17.90	monomer	HHblits	X-ray	1.50Å	0.28	0.52	Pollen allergen Phl p 4.0202
3js8.1.A	14.81	monomer	HHblits	X-ray	1.54Å	0.28	0.52	Cholesterol oxidase
3vte.1.A	17.90	monomer	HHblits	X-ray	2.75Å	0.28	0.52	Tetrahydrocannabinolic acid synthase
4dns.1.A	16.67	monomer	HHblits	X-ray	2.15Å	0.28	0.52	FAD-linked oxidoreductase BG60
3fw9.1.A	16.77	monomer	HHblits	X-ray	1.49Å	0.28	0.52	Reticuline oxidase
3tsh.1.A	18.01	monomer	HHblits	X-ray	1.90Å	0.28	0.52	Pollen allergen Phl p 4
4pvj.1.A	18.63	monomer	HHblits	X-ray	1.80Å	0.28	0.52	Pollen allergen Phl p 4.0202
4pvh.1.A	18.01	monomer	HHblits	X-ray	1.40Å	0.28	0.52	Pollen allergen Phl p 4.0202
3fw8.1.A	16.15	monomer	HHblits	X-ray	1.50Å	0.28	0.52	Reticuline oxidase
3fw7.1.A	16.15	monomer	HHblits	X-ray	1.82Å	0.28	0.52	Reticuline oxidase
3d2j.1.A	16.88	monomer	HHblits	X-ray	2.05Å	0.29	0.51	berberine bridge-forming enzyme
4pzf.1.A	16.15	monomer	HHblits	X-ray	2.20Å	0.28	0.52	Reticuline oxidase
1wve.1.A	13.50	hetero-oligomer	HHblits	X-ray	1.85Å	0.27	0.52	4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
4ud8.1.A	16.15	monomer	HHblits	X-ray	2.09Å	0.28	0.52	FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
4ud8.2.A	16.15	monomer	HHblits	X-ray	2.09Å	0.28	0.52	FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN
4ec3.1.A	16.88	monomer	HHblits	X-ray	2.65Å	0.28	0.51	Reticuline oxidase
3gsy.1.A	16.88	monomer	HHblits	X-ray	1.63Å	0.28	0.51	Reticuline oxidase; Berberine bridge-forming enzyme
2ipi.1.A	18.99	monomer	HHblits	X-ray	1.65Å	0.29	0.51	Aclacinomycin oxidoreductase (AknOx)
5d79.1.A	16.77	monomer	HHblits	X-ray	1.85Å	0.27	0.52	Berberine bridge enzyme-like protein
5epg.1.A	14.38	homo-dimer	HHblits	X-ray	3.39Å	0.28	0.51	Aldehyde oxidase
4uhw.1.A	13.75	homo-dimer	HHblits	X-ray	2.60Å	0.27	0.51	ALDEHYDE OXIDASE
3b9j.1.B	12.42	hetero-oligomer	HHblits	X-ray	2.30Å	0.27	0.52	xanthine oxidase
3pqb.1.A	17.50	homo-dimer	HHblits	X-ray	2.32Å	0.27	0.51	Putative oxidoreductase
2wdw.1.A	13.29	homo-dimer	HHblits	X-ray	3.21Å	0.28	0.51	PUTATIVE HEXOSE OXIDASE
5awv.1.C	13.29	homo-tetramer	HHblits	X-ray	1.93Å	0.28	0.51	Putative hexose oxidase
1fiq.1.B	11.18	hetero-oligomer	HHblits	X-ray	2.50Å	0.26	0.52	XANTHINE OXIDASE
3sr6.1.B	12.58	hetero-oligomer	HHblits	X-ray	2.10Å	0.27	0.51	Xanthine dehydrogenase/oxidase
3nvv.1.B	12.58	hetero-oligomer	HHblits	X-ray	1.82Å	0.27	0.51	Xanthine dehydrogenase/oxidase
2e3t.1.A	11.88	homo-dimer	HHblits	X-ray	2.28Å	0.26	0.51	Xanthine dehydrogenase/oxidase
2e3t.1.B	11.88	homo-dimer	HHblits	X-ray	2.28Å	0.26	0.51	Xanthine dehydrogenase/oxidase
2y3r.1.A	13.92	homo-dimer	HHblits	X-ray	1.79Å	0.27	0.51	TAML
4ytz.1.A	11.88	homo-dimer	HHblits	X-ray	2.30Å	0.26	0.51	Xanthine dehydrogenase/oxidase
4ytz.1.B	11.88	homo-dimer	HHblits	X-ray	2.30Å	0.26	0.51	Xanthine dehydrogenase/oxidase
4ysw.1.B	11.88	homo-dimer	HHblits	X-ray	1.99Å	0.26	0.51	Xanthine dehydrogenase/oxidase
5i1v.1.A	12.66	homo-dimer	HHblits	X-ray	1.84Å	0.27	0.51	CrmK
3an1.1.A	11.95	homo-dimer	HHblits	X-ray	1.73Å	0.26	0.51	Xanthine dehydrogenase/oxidase
3zyv.1.A	9.38	homo-dimer	HHblits	X-ray	2.55Å	0.26	0.51	AOX3
1wyg.1.A	11.95	monomer	HHblits	X-ray	2.60Å	0.26	0.51	Xanthine dehydrogenase/oxidase
3uni.1.A	11.32	homo-dimer	HHblits	X-ray	2.20Å	0.26	0.51	Xanthine dehydrogenase/oxidase
1n5x.1.A	11.32	homo-dimer	HHblits	X-ray	2.80Å	0.26	0.51	Xanthine Dehydrogenase
3amz.1.A	11.32	homo-dimer	HHblits	X-ray	2.10Å	0.26	0.51	Xanthine dehydrogenase/oxidase
3ax7.1.A	11.32	homo-dimer	HHblits	X-ray	2.34Å	0.26	0.51	Xanthine dehydrogenase/oxidase
2ckj.1.A	10.69	homo-dimer	HHblits	X-ray	3.59Å	0.26	0.51	XANTHINE OXIDOREDUCTASE
2e1q.1.A	10.69	homo-dimer	HHblits	X-ray	2.60Å	0.26	0.51	Xanthine dehydrogenase/oxidase
3hrd.1.C	17.45	hetero-oligomer	HHblits	X-ray	2.20Å	0.29	0.48	Nicotinate dehydrogenase FAD-subunit
2w3r.1.A	13.16	hetero-oligomer	HHblits	X-ray	2.90Å	0.27	0.49	XANTHINE DEHYDROGENASE
1jro.1.A	13.16	hetero-oligomer	HHblits	X-ray	2.70Å	0.27	0.49	xanthine dehydrogenase, chain A
1ffu.1.C	17.57	hetero-oligomer	HHblits	X-ray	2.35Å	0.28	0.48	CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
1ffv.1.C	17.69	hetero-oligomer	HHblits	X-ray	2.25Å	0.28	0.47	CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
1n62.1.C	16.22	hetero-oligomer	HHblits	X-ray	1.09Å	0.28	0.48	Carbon monoxide dehydrogenase medium chain
1zxi.1.C	14.77	hetero-oligomer	HHblits	X-ray	1.70Å	0.27	0.48	Carbon monoxide dehydrogenase medium chain
1t3q.1.C	11.56	hetero-oligomer	HHblits	X-ray	1.80Å	0.28	0.47	quinoline 2-oxidoreductase medium subunit
1e0y.1.A	16.55	homo-dimer	HHblits	X-ray	2.75Å	0.28	0.47	VANILLYL-ALCOHOL OXIDASE
1w1l.1.A	16.67	homo-dimer	HHblits	X-ray	2.70Å	0.28	0.46	VANILLYL-ALCOHOL OXIDASE
4zoh.1.B	12.33	hetero-oligomer	HHblits	X-ray	2.20Å	0.27	0.47	Putative oxidoreductase FAD-binding subunit
5mxj.1.A	17.65	homo-octamer	HHblits	X-ray	2.80Å	0.29	0.44	Vanillyl-alcohol oxidase
1f0x.1.A	18.46	monomer	HHblits	X-ray	1.90Å	0.28	0.42	D-LACTATE DEHYDROGENASE
4g3t.1.A	25.22	monomer	HHblits	X-ray	2.35Å	0.32	0.37	oxidoreductase DprE1
2yvs.1.A	16.83	homo-dimer	HHblits	X-ray	2.00Å	0.27	0.32	Glycolate oxidase subunit GlcE
2yvs.1.B	16.83	homo-dimer	HHblits	X-ray	2.00Å	0.27	0.32	Glycolate oxidase subunit GlcE
5d88.1.A	17.86	homo-dimer	HHblits	X-ray	1.66Å	0.28	0.27	Predicted protease of the collagenase family
1m1b.1.A	18.37	homo-tetramer	HHblits	X-ray	2.25Å	0.33	0.16	PHOSPHOENOLPYRUVATE PHOSPHOMUTASE
1s2v.1.A	18.37	homo-tetramer	HHblits	X-ray	2.10Å	0.33	0.16	Phosphoenolpyruvate phosphomutase
1s2w.1.A	18.37	monomer	HHblits	X-ray	1.69Å	0.33	0.16	Phosphoenolpyruvate phosphomutase
1s2u.1.A	18.37	homo-tetramer	HHblits	X-ray	2.00Å	0.33	0.16	Phosphoenolpyruvate phosphomutase
5unc.1.A	20.41	homo-tetramer	HHblits	X-ray	1.71Å	0.32	0.16	PHOSPHOENOLPYRUVATE PHOSPHOMUTASE
4iqd.1.A	14.29	homo-dimer	HHblits	X-ray	2.00Å	0.29	0.16	Carboxyvinyl-carboxyphosphonate phosphorylmutase
4iqe.1.B	14.29	homo-dimer	HHblits	X-ray	2.50Å	0.29	0.16	Carboxyvinyl-carboxyphosphonate phosphorylmutase
3cf4.1.B	9.52	hetero-oligomer	HHblits	X-ray	2.00Å	0.25	0.14	Acetyl-CoA decarboxylase/synthase epsilon subunit
1wn2.1.A	9.76	homo-dimer	HHblits	X-ray	1.20Å	0.25	0.13	Peptidyl-tRNA hydrolase
2d3k.1.A	9.76	homo-dimer	HHblits	X-ray	1.90Å	0.25	0.13	Peptidyl-tRNA hydrolase
2zv3.1.A	12.50	homo-dimer	HHblits	X-ray	2.10Å	0.26	0.13	Peptidyl-tRNA hydrolase
2zv3.3.B	12.50	homo-dimer	HHblits	X-ray	2.10Å	0.26	0.13	Peptidyl-tRNA hydrolase
2zv3.4.A	12.50	homo-dimer	HHblits	X-ray	2.10Å	0.26	0.13	Peptidyl-tRNA hydrolase
2zv3.4.B	12.50	homo-dimer	HHblits	X-ray	2.10Å	0.26	0.13	Peptidyl-tRNA hydrolase
1xty.1.A	4.88	homo-dimer	HHblits	X-ray	1.80Å	0.25	0.13	Peptidyl-tRNA hydrolase
1rlk.1.A	10.00	monomer	HHblits	X-ray	1.95Å	0.24	0.13	Hypothetical protein Ta0108
1q7s.1.A	7.89	monomer	HHblits	X-ray	2.00Å	0.26	0.12	bit1
1q7s.2.A	7.89	monomer	HHblits	X-ray	2.00Å	0.26	0.12	bit1
3erj.1.A	15.38	homo-dimer	HHblits	X-ray	1.80Å	0.24	0.13	Peptidyl-tRNA hydrolase
3erj.1.B	15.38	homo-dimer	HHblits	X-ray	1.80Å	0.24	0.13	Peptidyl-tRNA hydrolase
1rzw.1.A	15.38	monomer	HHblits	NMR	NA	0.24	0.13	Protein AF2095(GR4)
2ki0.1.A	15.63	monomer	HHblits	NMR	NA	0.28	0.10	DS119
2lnd.1.A	12.90	monomer	HHblits	NMR	NA	0.29	0.10	DE NOVO DESIGNED PROTEIN, PFK fold
2lvb.1.A	13.33	monomer	HHblits	NMR	NA	0.29	0.10	DE NOVO DESIGNED PFK fold PROTEIN