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SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "J0LRF5" submitted to SWISS-MODEL workspace on Oct. 17, 2017, 6:45 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 170 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	0.44	-4.27

QMEAN	-4.27
Cβ	-3.62
All Atom	-1.50
Solvation	0.45
Torsion	-3.70

Template	Seq Identity	Oligo-state	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
3zl8.1.A	22.59	monomer	HHblits	X-ray	1.65Å	0.31	149 - 489	0.67	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE

Ligand	Added to Model	Description
ADP	✕ - Binding site not conserved.	ADENOSINE-5'-DIPHOSPHATE
GOL	✕ - Not biologically relevant.	GLYCEROL

Target    MQSLSWLNLAFRWLFITGLGYYIMTLLQWYHYSVFRILTKHHKMRWHGIYFLLPLGVFILSYAFKMPFVFDFFCGVIQMP
3zl8.1.A  --------------------------------------------------------------------------------

Target    MLIVWAKRNDKPLVFTPRVKRFFIFLLLFLILHEILNTELVPLNGISLALGYLCLFIFVLSASLIFEKVLSKRYLQTAKD
3zl8.1.A  --------------------------------------------------------------------SSVDTLAKLARE

Target    KIASLKNLKVIAITGSFGKTSTKNFLLQILQTTFNAHASPKSVNTLLGIANDINQNLDDKSEIYIAEAGARNKGDIKEIT
3zl8.1.A  KLGNF-SGTVVGVTGSSGKTTTKEILYNLLKNKRSVFKTPGNMNTEYGLPLSIL-NDYKGEEILVLEMAASRPGDIAHLC

Target    RLIEPHLAVIAEVGEQHLEYFKTLENICETKAELLDSKR-LEKAFCYSVEKIKPYAPKDSPLIDV-SS---L--VKNIQS
3zl8.1.A  KIAPPDVAVLLNVGSAHLEFFGTRERIMETKMEIIKHSKENAIAVTLFDDPDLRKEVPRYRNTLFFGKEGGDSVLKDWWY

Target    TLKGTSFEMLLDSVWE--SFETK-ILGKFNAYNIASAILIAKHLGLETERIKRLVLELNPIAHRLQLLEVNQKIIIDDSF
3zl8.1.A  YEGSTIAEFE-AF-DSLFTVKLSGYWNGGQLLNIAASLCVMRTLGETVDIF--DLASLKTVPGRFNVREKKGVLIVDDTY

Target    NGNLKGMLEGIRLASLHKGRKVIVTPGLV---ESNVESNEALAQKIDGVFDVAIITGELNSKTIASKLKTPQKILLKDKA
3zl8.1.A  NASPEAFQTSIEALLRFPGKKFAVVGAMKELGERSKEFHEELGERLNVLDGVYVFLSEPEAEW-IKSKKI--ILKSDDPE

Target    QLENILQATTIQGDLILFANDAPNYI
3zl8.1.A  KIAKDLATRVKKGDVVLFKASR----

Model #02	File	Built with	Oligo-State	Ligands	GMQE	QMEAN
	PDB	ProMod3 Version 1.0.2.	MONOMER	None	0.44	-3.99

QMEAN	-3.99
Cβ	-1.34
All Atom	-0.50
Solvation	-0.07
Torsion	-3.79

Template	Seq Identity	Oligo-state	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
3zm5.1.A	20.60	monomer	HHblits	X-ray	2.94Å	0.31	150 - 490	0.68	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE

Ligand	Added to Model	Description
IGM	✕ - Binding site not conserved.	2,4-BIS(CHLORANYL)-N-[3-CYANO-6-[(4-HYDROXYPHENYL)METHYL]-5,7-DIHYDRO-4H-THIENO[2,3-C]PYRIDIN-2-YL]-5-MORPHOLIN-4-YLSULFONYL-BENZAMIDE

Target    MQSLSWLNLAFRWLFITGLGYYIMTLLQWYHYSVFRILTKHHKMRWHGIYFLLPLGVFILSYAFKMPFVFDFFCGVIQMP
3zm5.1.A  --------------------------------------------------------------------------------

Target    MLIVWAKRNDKPLVFTPRVKRFFIFLLLFLILHEILNTELVPLNGISLALGYLCLFIFVLSASLIFEKVLSKRYLQTAKD
3zm5.1.A  ---------------------------------------------------------------------VLTAFQSLASY

Target    KIASLKNLKVIAITGSFGKTSTKNFLLQILQTTFNAHASPKSVNTLLGIANDINQNLDDKSEIYIAEAGARNKGDIKEIT
3zm5.1.A  YLEK-TTVDVFAVTGSNGKTTTKDMLAHLLSTRYKTYKTQGNYNNEIGLPYTVL-HMPEGTEKLVLEMGQDHLGDIHLLS

Target    RLIEPHLAVIAEVGEQHLEYFKTLENICETKAELLDSKR-LEKAFCYSVEKIKPYAP-KDSPLIDVSSL----VKNIQST
3zm5.1.A  ELARPKTAIVTLVGEAHLAFFKDRSEIAKGKMQIADGMASGSLLLAPADPIVE-DYLPIDKKVVRFGQGAELEITDLVER

Target    LKGTSFEMLLDSVWESFETKILGKFNAYNIASAILIAKHLGLETERIKRLVLELNPIAHRLQLLEV-NQKIIIDDSFNGN
3zm5.1.A  KDSLTFKANFLEQ--ALDLPVTGKYNATNAMIASYVALQEGVSEEQIRLAFQHLELTRNRTEWKKAANGADILSDVYNAN

Target    LKGMLEGIRLASLH---K-GRKVIVTPGLV---ESNVESNEALAQKIDGV-FDVAIITGELNSKTIASKLKT----PQKI
3zm5.1.A  PTAMKLILETFSAIPANEGGKKIAVLADMKELGDQSVQLHNQMILSLSPDVLDIVIFYGEDIAQLA-QLASQMFPIGHVY

Target    LLKD------KAQLENILQATTIQGDLILFANDAPNYI
3zm5.1.A  YFKKTEDQDQFEDLVKQVKESLGAHDQILLKGSNS---

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 10 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 162 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.

MQSLSWLNLAFRWLFITGLGYYIMTLLQWYHYSVFRILTKHHKMRWHGIYFLLPLGVFILSYAFKMPFVFDFFCGVIQMPMLIVWAKRNDKPLVFTPRVK
RFFIFLLLFLILHEILNTELVPLNGISLALGYLCLFIFVLSASLIFEKVLSKRYLQTAKDKIASLKNLKVIAITGSFGKTSTKNFLLQILQTTFNAHASP
KSVNTLLGIANDINQNLDDKSEIYIAEAGARNKGDIKEITRLIEPHLAVIAEVGEQHLEYFKTLENICETKAELLDSKRLEKAFCYSVEKIKPYAPKDSP
LIDVSSLVKNIQSTLKGTSFEMLLDSVWESFETKILGKFNAYNIASAILIAKHLGLETERIKRLVLELNPIAHRLQLLEVNQKIIIDDSFNGNLKGMLEG
IRLASLHKGRKVIVTPGLVESNVESNEALAQKIDGVFDVAIITGELNSKTIASKLKTPQKILLKDKAQLENILQATTIQGDLILFANDAPNYI

Table T2:

Template	Seq Identity	Oligo-state	Found by	Method	Resolution	Seq Similarity	Coverage	Description
2am2.1.A	20.54	monomer	HHblits	X-ray	2.80Å	0.31	0.68	UDP-N-acetylmuramoylalanine-D-glutamyl-lysine-D-alanyl-D-alanine ligase, MurF protein
3zm5.1.A	20.60	monomer	HHblits	X-ray	2.94Å	0.31	0.68	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
4qf5.1.A	22.75	monomer	HHblits	X-ray	2.80Å	0.31	0.68	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
4qdi.1.A	22.75	monomer	HHblits	X-ray	1.80Å	0.31	0.68	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
4ziy.1.A	22.82	monomer	HHblits	X-ray	1.85Å	0.31	0.68	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
4cvl.1.A	23.58	monomer	HHblits	X-ray	2.98Å	0.31	0.68	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
4cvm.1.A	23.58	monomer	HHblits	X-ray	2.06Å	0.31	0.68	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D- ALANINE LIGASE
3zl8.1.A	22.59	monomer	HHblits	X-ray	1.65Å	0.31	0.67	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
1gg4.1.A	20.96	monomer	HHblits	X-ray	2.30Å	0.31	0.68	UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE
4c12.1.A	18.64	homo-dimer	HHblits	X-ray	1.80Å	0.29	0.69	UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--L-LYSINE LIGASE
4bub.1.A	16.67	monomer	HHblits	X-ray	2.90Å	0.29	0.68	UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--LD-LYSINE LIGASE
4bub.2.A	16.67	monomer	HHblits	X-ray	2.90Å	0.29	0.68	UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--LD-LYSINE LIGASE
1e8c.1.A	16.32	monomer	HHblits	X-ray	2.00Å	0.29	0.68	UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
3zl8.1.A	32.24	monomer	BLAST	X-ray	1.65Å	0.36	0.62	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
2xja.1.A	14.58	monomer	HHblits	X-ray	3.00Å	0.28	0.68	UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
2wtz.1.A	14.58	monomer	HHblits	X-ray	3.00Å	0.28	0.68	UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
1o5z.1.A	19.49	monomer	HHblits	X-ray	2.10Å	0.30	0.63	folylpolyglutamate synthase/dihydrofolate synthase
3hn7.1.A	17.30	monomer	HHblits	X-ray	1.65Å	0.28	0.65	UDP-N-acetylmuramate-L-alanine ligase
5a5f.1.A	16.04	monomer	HHblits	X-ray	1.90Å	0.28	0.65	UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
1p3d.1.A	18.27	monomer	HHblits	X-ray	1.70Å	0.29	0.63	UDP-N-acetylmuramate--alanine ligase
1gqq.1.A	18.27	homo-dimer	HHblits	X-ray	3.10Å	0.29	0.63	UDP-N-ACETYLMURAMATE-L-ALANINE LIGASE
1gqq.1.B	18.27	homo-dimer	HHblits	X-ray	3.10Å	0.29	0.63	UDP-N-ACETYLMURAMATE-L-ALANINE LIGASE
1p31.1.A	18.27	monomer	HHblits	X-ray	1.85Å	0.29	0.63	UDP-N-acetylmuramate--alanine ligase
1gqy.1.B	18.27	homo-dimer	HHblits	X-ray	1.80Å	0.29	0.63	UDP-N-ACETYLMURAMATE-L-ALANINE LIGASE
1gqy.1.A	18.27	homo-dimer	HHblits	X-ray	1.80Å	0.29	0.63	UDP-N-ACETYLMURAMATE-L-ALANINE LIGASE
4hv4.1.A	17.57	monomer	HHblits	X-ray	2.25Å	0.29	0.63	UDP-N-acetylmuramate--L-alanine ligase
4hv4.2.A	17.57	monomer	HHblits	X-ray	2.25Å	0.29	0.63	UDP-N-acetylmuramate--L-alanine ligase
2f00.1.A	17.89	homo-dimer	HHblits	X-ray	2.50Å	0.29	0.63	UDP-N-acetylmuramate--L-alanine ligase
2vor.1.A	16.29	monomer	HHblits	X-ray	2.30Å	0.29	0.63	FOLYLPOLYGLUTAMATE SYNTHASE PROTEIN FOLC
2gcb.1.A	16.08	monomer	HHblits	X-ray	2.30Å	0.28	0.63	Folylpolyglutamate synthase
3nrs.1.A	15.71	monomer	HHblits	X-ray	1.80Å	0.28	0.63	Dihydrofolate:folylpolyglutamate synthetase
3pyz.1.A	15.71	monomer	HHblits	X-ray	2.10Å	0.28	0.63	Bifunctional folylpolyglutamate synthase/dihydrofolate synthase
3lk7.1.A	17.59	monomer	HHblits	X-ray	1.50Å	0.29	0.62	UDP-N-acetylmuramoylalanine--D-glutamate ligase
1fgs.1.A	16.45	monomer	HHblits	X-ray	2.40Å	0.28	0.63	FOLYLPOLYGLUTAMATE SYNTHETASE
1jbw.1.A	16.45	monomer	HHblits	X-ray	1.85Å	0.28	0.63	FOLYLPOLYGLUTAMATE SYNTHASE
1jbv.1.A	16.45	monomer	HHblits	X-ray	1.95Å	0.28	0.63	FOLYLPOLYGLUTAMATE SYNTHASE
2gc6.1.A	16.45	monomer	HHblits	X-ray	1.90Å	0.28	0.63	Folylpolyglutamate synthase
1uag.1.A	16.67	monomer	HHblits	X-ray	1.95Å	0.29	0.62	UDP-N-ACETYLMURAMOYL-L-ALANINE/:D-GLUTAMATE LIGASE
1eeh.1.A	16.67	monomer	HHblits	X-ray	1.90Å	0.29	0.62	UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
2uag.1.A	16.67	monomer	HHblits	X-ray	1.70Å	0.29	0.62	PROTEIN (UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE)
1e0d.1.A	16.67	monomer	HHblits	X-ray	2.40Å	0.29	0.62	UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
5a5e.1.A	16.67	monomer	HHblits	X-ray	1.84Å	0.29	0.62	UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
2xpc.1.A	16.67	monomer	HHblits	X-ray	1.49Å	0.29	0.62	UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
2y67.1.A	16.67	monomer	HHblits	X-ray	1.85Å	0.29	0.62	UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
4buc.1.A	13.27	monomer	HHblits	X-ray	2.17Å	0.28	0.63	UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
4buc.2.A	13.27	monomer	HHblits	X-ray	2.17Å	0.28	0.63	UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
2gc5.1.A	17.05	monomer	HHblits	X-ray	1.85Å	0.28	0.62	Folylpolyglutamate synthase
1w7k.1.A	16.61	monomer	HHblits	X-ray	2.10Å	0.28	0.62	FOLC BIFUNCTIONAL PROTEIN
1w78.1.A	16.61	monomer	HHblits	X-ray	1.82Å	0.28	0.62	FOLC BIFUNCTIONAL PROTEIN
2gca.1.A	17.05	monomer	HHblits	X-ray	2.40Å	0.28	0.62	Folylpolyglutamate synthase
1j6u.1.A	13.91	monomer	HHblits	X-ray	2.30Å	0.29	0.61	UDP-N-acetylmuramate-alanine ligase MurC
2am2.1.A	28.52	monomer	BLAST	X-ray	2.80Å	0.35	0.55	UDP-N-acetylmuramoylalanine-D-glutamyl-lysine-D-alanyl-D-alanine ligase, MurF protein
3zm5.1.A	28.52	monomer	BLAST	X-ray	2.94Å	0.35	0.55	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
4cvl.1.A	28.96	monomer	BLAST	X-ray	2.98Å	0.34	0.53	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
4cvm.1.A	28.96	monomer	BLAST	X-ray	2.06Å	0.34	0.53	UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D- ALANINE LIGASE
1gg4.1.A	25.68	monomer	BLAST	X-ray	2.30Å	0.34	0.52	UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE
4ziy.1.A	28.69	monomer	BLAST	X-ray	1.85Å	0.34	0.48	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
4qf5.1.A	28.69	monomer	BLAST	X-ray	2.80Å	0.34	0.48	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
4qdi.1.A	28.69	monomer	BLAST	X-ray	1.80Å	0.34	0.48	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
4c12.1.A	29.58	homo-dimer	BLAST	X-ray	1.80Å	0.35	0.43	UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--L-LYSINE LIGASE
3eag.1.A	16.10	homo-dimer	HHblits	X-ray	2.55Å	0.29	0.42	UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase
3eag.1.B	16.10	homo-dimer	HHblits	X-ray	2.55Å	0.29	0.42	UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase
5vvw.1.A	18.88	homo-tetramer	HHblits	X-ray	2.30Å	0.29	0.40	UDP-N-acetylmuramate--L-alanine ligase
2h07.1.A	17.61	homo-hexamer	HHblits	X-ray	2.20Å	0.28	0.29	Ribose-phosphate pyrophosphokinase I
2h07.1.B	17.61	homo-hexamer	HHblits	X-ray	2.20Å	0.28	0.29	Ribose-phosphate pyrophosphokinase I
4lyg.1.A	18.31	homo-hexamer	HHblits	X-ray	3.00Å	0.28	0.29	Ribose-phosphate pyrophosphokinase 1
3mvn.1.A	16.81	monomer	HHblits	X-ray	1.90Å	0.27	0.23	UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-medo-diaminopimelate ligase
2mr6.1.A	12.20	monomer	HHblits	NMR	NA	0.26	0.17	De novo designed Protein OR462
1mw7.1.A	16.67	monomer	HHblits	X-ray	2.00Å	0.28	0.12	HYPOTHETICAL PROTEIN HP0162
5ekz.1.A	4.92	monomer	HHblits	X-ray	2.00Å	0.24	0.12	Translational activator of cytochrome c oxidase 1
1w36.1.C	28.57	hetero-oligomer	HHblits	X-ray	3.10Å	0.31	0.07	EXODEOXYRIBONUCLEASE V ALPHA CHAIN
3k70.1.C	28.57	hetero-oligomer	HHblits	X-ray	3.59Å	0.31	0.07	Exodeoxyribonuclease V alpha chain
3dm9.1.A	33.33	homo-hexamer	HHblits	X-ray	2.20Å	0.32	0.06	Signal recognition particle receptor
3e70.1.A	33.33	monomer	HHblits	X-ray	1.97Å	0.32	0.06	Signal recognition particle receptor
3dmd.1.F	33.33	homo-hexamer	HHblits	X-ray	2.21Å	0.32	0.06	Signal recognition particle receptor
3dmd.1.E	33.33	homo-hexamer	HHblits	X-ray	2.21Å	0.32	0.06	Signal recognition particle receptor
5l3w.1.A	26.67	monomer	HHblits	X-ray	2.40Å	0.31	0.06	Signal recognition particle receptor FtsY
5l3s.1.B	26.67	hetero-oligomer	HHblits	X-ray	1.90Å	0.31	0.06	Signal recognition particle receptor FtsY
5l3s.2.B	26.67	hetero-oligomer	HHblits	X-ray	1.90Å	0.31	0.06	Signal recognition particle receptor FtsY
5l3s.3.B	26.67	hetero-oligomer	HHblits	X-ray	1.90Å	0.31	0.06	Signal recognition particle receptor FtsY
5l3s.4.B	26.67	hetero-oligomer	HHblits	X-ray	1.90Å	0.31	0.06	Signal recognition particle receptor FtsY
1j8m.1.A	31.03	monomer	HHblits	X-ray	2.00Å	0.33	0.06	SIGNAL RECOGNITION 54 KDA PROTEIN
1qzw.1.B	24.14	monomer	HHblits	X-ray	4.10Å	0.32	0.06	Signal recognition 54 kDa protein
1qzx.1.A	24.14	monomer	HHblits	X-ray	4.00Å	0.32	0.06	Signal recognition 54 kDa protein
3kl4.1.A	24.14	hetero-oligomer	HHblits	X-ray	3.50Å	0.32	0.06	Signal recognition 54 kDa protein
5l3s.1.A	24.14	hetero-oligomer	HHblits	X-ray	1.90Å	0.32	0.06	Signal recognition particle 54 kDa protein
5l3s.4.A	24.14	hetero-oligomer	HHblits	X-ray	1.90Å	0.32	0.06	Signal recognition particle 54 kDa protein
4c7o.1.B	27.59	hetero-oligomer	HHblits	X-ray	2.60Å	0.31	0.06	SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY
2j7p.1.A	20.00	hetero-oligomer	HHblits	X-ray	1.97Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
3ng1.1.A	20.00	monomer	HHblits	X-ray	2.30Å	0.28	0.06	SIGNAL SEQUENCE RECOGNITION PROTEIN FFH
2cnw.1.A	20.00	hetero-oligomer	HHblits	X-ray	2.39Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2cnw.3.A	20.00	hetero-oligomer	HHblits	X-ray	2.39Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2xkv.1.A	20.00	hetero-oligomer	HHblits	EM	13.50Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
1ffh.1.A	20.00	monomer	HHblits	X-ray	2.05Å	0.28	0.06	FFH
1rj9.1.B	20.00	hetero-oligomer	HHblits	X-ray	1.90Å	0.28	0.06	Signal recognition particle protein
2j45.1.A	20.00	monomer	HHblits	X-ray	1.14Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2j45.2.A	20.00	monomer	HHblits	X-ray	1.14Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2j46.1.A	20.00	monomer	HHblits	X-ray	1.14Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2j46.2.A	20.00	monomer	HHblits	X-ray	1.14Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
1o87.1.A	20.00	monomer	HHblits	X-ray	2.10Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
1o87.2.A	20.00	monomer	HHblits	X-ray	2.10Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2c04.1.A	20.00	monomer	HHblits	X-ray	1.15Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2c04.2.A	20.00	monomer	HHblits	X-ray	1.15Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2c03.1.A	20.00	monomer	HHblits	X-ray	1.24Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2c03.2.A	20.00	monomer	HHblits	X-ray	1.24Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
2ng1.1.A	20.00	monomer	HHblits	X-ray	2.02Å	0.28	0.06	SIGNAL SEQUENCE RECOGNITION PROTEIN FFH
1ls1.1.A	20.00	monomer	HHblits	X-ray	1.10Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
1jpj.1.A	20.00	monomer	HHblits	X-ray	2.30Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
1jpn.1.A	20.00	monomer	HHblits	X-ray	1.90Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
1jpn.2.A	20.00	monomer	HHblits	X-ray	1.90Å	0.28	0.06	SIGNAL RECOGNITION PARTICLE PROTEIN
5nco.1.c	27.59	hetero-oligomer	HHblits	EM	4.80Å	0.31	0.06	Signal recognition particle receptor FtsY
2xxa.1.B	27.59	hetero-oligomer	HHblits	X-ray	3.94Å	0.31	0.06	SRP RECEPTOR FTSY
2qy9.1.A	27.59	monomer	HHblits	X-ray	1.90Å	0.31	0.06	Cell division protein ftsY
1fts.1.A	27.59	monomer	HHblits	X-ray	2.20Å	0.31	0.06	FTSY
2yhs.1.A	27.59	monomer	HHblits	X-ray	1.60Å	0.31	0.06	CELL DIVISION PROTEIN FTSY
2j28.1.H	24.14	hetero-oligomer	HHblits	EM	8.00Å	0.31	0.06	SIGNAL RECOGNITION PARTICLE 54
5nco.1.9	24.14	hetero-oligomer	HHblits	EM	4.80Å	0.30	0.06	Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein
5gad.1.7	24.14	hetero-oligomer	HHblits	EM	NA	0.30	0.06	Signal recognition particle protein Ffh
5l3r.1.A	27.59	hetero-oligomer	HHblits	X-ray	2.50Å	0.30	0.06	Signal recognition particle 54 kDa protein, chloroplastic
3ug7.1.A	16.67	homo-tetramer	HHblits	X-ray	2.90Å	0.27	0.06	arsenical pump-driving ATPase
3ug6.1.A	16.67	homo-tetramer	HHblits	X-ray	3.30Å	0.27	0.06	arsenical pump-driving ATPase
4v03.1.A	28.57	homo-dimer	HHblits	X-ray	1.90Å	0.31	0.06	SITE-DETERMINING PROTEIN
2ffh.1.A	20.69	monomer	HHblits	X-ray	3.20Å	0.28	0.06	PROTEIN (FFH)
5l3q.1.A	33.33	hetero-oligomer	HHblits	X-ray	3.20Å	0.32	0.05	Signal recognition particle 54 kDa protein
4ue5.1.D	33.33	hetero-oligomer	HHblits	EM	9.00Å	0.32	0.05	SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN
4pwx.1.A	13.79	hetero-oligomer	HHblits	X-ray	5.40Å	0.27	0.06	ATPase GET3
2v3c.1.B	34.62	hetero-oligomer	HHblits	X-ray	2.50Å	0.35	0.05	SIGNAL RECOGNITION 54 KDA PROTEIN
2v3c.2.B	34.62	hetero-oligomer	HHblits	X-ray	2.50Å	0.35	0.05	SIGNAL RECOGNITION 54 KDA PROTEIN
3ndb.1.B	34.62	hetero-oligomer	HHblits	X-ray	3.00Å	0.35	0.05	Signal recognition 54 kDa protein
3io3.1.A	21.43	monomer	HHblits	X-ray	1.80Å	0.29	0.06	DEHA2D07832p
3zq6.1.A	14.29	homo-dimer	HHblits	X-ray	2.11Å	0.28	0.06	PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
3zq6.1.B	14.29	homo-dimer	HHblits	X-ray	2.11Å	0.28	0.06	PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
3zq6.2.A	14.29	homo-dimer	HHblits	X-ray	2.11Å	0.28	0.06	PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
3zq6.2.B	14.29	homo-dimer	HHblits	X-ray	2.11Å	0.28	0.06	PUTATIVE ARSENICAL PUMP-DRIVING ATPASE
2j37.1.G	34.62	hetero-oligomer	HHblits	EM	8.00Å	0.33	0.05	SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (SRP54)
4xwo.1.A	14.29	hetero-oligomer	HHblits	X-ray	2.75Å	0.27	0.06	ATPase GET3
4xtr.1.B	14.29	hetero-oligomer	HHblits	X-ray	2.05Å	0.27	0.06	ATPase GET3
4xtr.1.A	14.29	hetero-oligomer	HHblits	X-ray	2.05Å	0.27	0.06	ATPase GET3
4xvu.1.B	14.29	hetero-oligomer	HHblits	X-ray	2.35Å	0.27	0.06	ATPase GET3
4xvu.1.G	14.29	hetero-oligomer	HHblits	X-ray	2.35Å	0.27	0.06	ATPase GET3
4xvu.1.H	14.29	hetero-oligomer	HHblits	X-ray	2.35Å	0.27	0.06	ATPase GET3
4xvu.1.A	14.29	hetero-oligomer	HHblits	X-ray	2.35Å	0.27	0.06	ATPase GET3
3a4l.1.A	32.00	homo-dimer	HHblits	X-ray	1.80Å	0.35	0.05	L-seryl-tRNA(Sec) kinase
3a4l.1.B	32.00	homo-dimer	HHblits	X-ray	1.80Å	0.35	0.05	L-seryl-tRNA(Sec) kinase
3am1.1.C	32.00	homo-dimer	HHblits	X-ray	2.40Å	0.35	0.05	L-seryl-tRNA(Sec) kinase
3jaj.45.A	36.00	monomer	HHblits	EM	NA	0.34	0.05	SRP54
3jan.45.A	36.00	monomer	HHblits	EM	NA	0.34	0.05	SRP54
4c7o.1.A	28.00	hetero-oligomer	HHblits	X-ray	2.60Å	0.32	0.05	SIGNAL RECOGNITION PARTICLE PROTEIN
4c7o.2.A	28.00	hetero-oligomer	HHblits	X-ray	2.60Å	0.32	0.05	SIGNAL RECOGNITION PARTICLE PROTEIN
1j8y.1.A	28.00	monomer	HHblits	X-ray	2.00Å	0.32	0.05	SIGNAL RECOGNITION 54 KDA PROTEIN
2ax4.1.A	28.00	homo-dimer	HHblits	X-ray	2.50Å	0.31	0.05	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
2xxa.1.A	29.17	hetero-oligomer	HHblits	X-ray	3.94Å	0.33	0.05	SIGNAL RECOGNITION PARTICLE PROTEIN
2xxa.2.A	29.17	hetero-oligomer	HHblits	X-ray	3.94Å	0.33	0.05	SIGNAL RECOGNITION PARTICLE PROTEIN
3r8f.1.A	28.00	homo-tetramer	HHblits	X-ray	3.37Å	0.29	0.05	Chromosomal replication initiator protein dnaA
1l8q.1.A	28.00	monomer	HHblits	X-ray	2.70Å	0.29	0.05	Chromosomal replication initiator protein dnaA
4d81.1.A	25.00	monomer	HHblits	X-ray	2.40Å	0.31	0.05	AAA ATPASE, CENTRAL DOMAIN PROTEIN
1xd9.1.A	25.00	homo-dimer	HHblits	X-ray	2.80Å	0.31	0.05	Nitrogenase iron protein 1
1xdb.1.A	25.00	homo-dimer	HHblits	X-ray	2.80Å	0.31	0.05	Nitrogenase iron protein 1
3kjg.2.A	26.09	homo-dimer	HHblits	X-ray	2.30Å	0.33	0.05	CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
3kjg.1.A	26.09	monomer	HHblits	X-ray	2.30Å	0.33	0.05	CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
3kji.1.A	26.09	homo-dimer	HHblits	X-ray	2.13Å	0.33	0.05	CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
3kji.2.A	26.09	homo-dimer	HHblits	X-ray	2.13Å	0.33	0.05	CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
3kjh.1.A	26.09	homo-dimer	HHblits	X-ray	1.90Å	0.33	0.05	CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
3kje.1.A	26.09	monomer	HHblits	X-ray	2.30Å	0.33	0.05	CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
4rfv.1.A	26.09	homo-dimer	HHblits	X-ray	1.69Å	0.31	0.05	Bifunctional enzyme CysN/CysC
5ftf.1.A	35.00	monomer	HHblits	X-ray	2.41Å	0.36	0.04	TPR DOMAIN PROTEIN
5ftb.1.A	35.00	monomer	HHblits	X-ray	1.38Å	0.36	0.04	TPR DOMAIN PROTEIN
5ftc.1.A	35.00	monomer	HHblits	X-ray	2.27Å	0.36	0.04	TPR DOMAIN PROTEIN
5ftd.1.A	35.00	monomer	HHblits	X-ray	1.70Å	0.36	0.04	TPR DOMAIN PROTEIN
5fte.1.A	35.00	monomer	HHblits	X-ray	3.19Å	0.36	0.04	TPR DOMAIN PROTEIN