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SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "UniProtACP70922" submitted to SWISS-MODEL workspace on April 24, 2018, 4:07 a.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:

Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T.G., Bertoni, M., Bordoli, L., Schwede, T. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42, W252-W258 (2014).
Guex, N., Peitsch, M.C., Schwede, T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis 30, S162-S173 (2009).
Bienert, S., Waterhouse, A., de Beer, T.A., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
Benkert, P., Biasini, M., Schwede, T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27, 343-350 (2011).
Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., Schwede, T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports 7 (2017).

Results

The SWISS-MODEL template library (SMTL version 2018-04-18, PDB release 2018-04-13) was searched with BLAST (Camacho et al.) and HHBlits (Remmert et al.) for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 369 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 1.1.0.	monomer	1 x ZN: ZINC ION;	0.71	-1.72

QMEAN	-1.72
Cβ	-0.78
All Atom	1.51
Solvation	1.98
Torsion	-2.00

Template	Seq Identity	Oligo-state	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
3ce2.1.A	37.16	monomer	HHblits	X-ray	2.60Å	0.39	29 - 622	0.94	Putative peptidase

Ligand	Added to Model	Description
ZN	✓	ZINC ION
ZN	✕ - Binding site not conserved.	ZINC ION
ZN	✕ - Not biologically relevant.	ZINC ION
ZN	✕ - Binding site not conserved.	ZINC ION
ZN	✕ - Binding site not conserved.	ZINC ION
ZN	✕ - Clashing with protein.	ZINC ION

Target    MRNSCFFNWLESKKTRGITMAEEKKANQLPDRSEVKAEDTWRLEDIFPSDEAWNKEFQAVK------ELIPNLSKYKGKL
3ce2.1.A  ----------------------------VRPRSEISPQDCWDITPLYLNRKAWKADLDSFGLKTDGSPTWPALQATQYQL

Target    ADSADHLYEALTYQDKVMERLGRLYTYAHMRSDQDTGNSFYQGLNDKAGNLYTQAASATAYLVPEILSIEEDKLQQFILE
3ce2.1.A  -DNSESLLSLLTTLFSIERKLNKLYVYAHLTHDQDITNQEGIADLKSITHLHTLFAEETSWVQPALTSLSESLIAQHLSA

Target    KEELKLYSHAIEEITKERPHVLSEKEEALLAEASEVLGSSSNTFSVLNNADITFPSIKDEDGNEKQITHGNFINFLESEN
3ce2.1.A  -PCLAPYRFYLEKIFRLSIHTGTPGEEKILASAFTPLEVASKAFSSLSDSEIPFGQATDSEGNSHPLSHALASLYMQSTD

Target    REVRKNAFDAVYKTYGQYKNTMATTLSGTVKKDNFYARVKKYKSAREAALSNNSIPEEVYDNLVKTINKHLPLLHRYIAL
3ce2.1.A  RELRKTSYLAQCERYHSYRHTFANLLNGKIQAHVFYAKNKRYNSCLQAALYHNNIPTTVYTNLIDIVKKNSSLITKYFSI

Target    RKKVLELDEVHIYDLYTPLVKDAGMKVTYEEAKDYMLKGLAPLGEEYASILKEGL-ENRWVDVYENKGKRNGAYSSGAYG
3ce2.1.A  KQRCLNLKDFHFYDVYAPLSQSKEKKYTFQEAVDLIYTSLSPLGTEYIDTLKQGLTTQGWVDKYENLNKRSGAYSSGCYD

Target    TNPYILMNWHNNVNNLFTLVHEFGHSVHSYYTRKHQPYPYGNYSIFVAEVASTTNEALLGEYLLNNLEDEKQRLYILNHM
3ce2.1.A  SHPYVLLNYTGTLYDVSVIAHEGGHSMHSYFSRKHQPFHDAQYPIFLAEIASTLNEMLLMDSMLKESDSKEEKITILTRC

Target    LEGFRGTVFRQTMFAEFEHLIHTKAQEGEPLTPELLTKVYYDLNKKYFGDGMVIDKEIGLEWSRIPHFYYNYYVYQYATG
3ce2.1.A  LDTIFSTLFRQVLFASFEYDIHHAAEHGVPLTEEYLSSTYKNLQNEFYGEIITFDVLSNIEWARIPHFYYNFYVYQYATG

Target    YSAAQALSSQILKEGKPAVDRYIDFLKAGSSQYPIDVLKKAGVDMTSPEPIEAACKMFEEKLDEMEELLMKVKQS
3ce2.1.A  IIAALCFLEKILNNEDNALNSYLNFLKSGGSDFPLEILKKSGLDMGTVEPIQKAFCFIEKKIQELSSLI------

Materials and Methods

Template Search

Template search with BLAST and HHBlits has been performed against the SWISS-MODEL template library (SMTL, last update: 2018-04-18, last included PDB release: 2018-04-13).

The target sequence was searched with BLAST against the primary amino acid sequence contained in the SMTL. A total of 6 templates were found.

An initial HHblits profile has been built using the procedure outlined in (Remmert et al.), followed by 1 iteration of HHblits against NR20. The obtained profile has then be searched against all profiles of the SMTL. A total of 428 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.).

Model Quality Estimation

The global and per-residue model quality has been assessed using the QMEAN scoring function (Benkert et al.) . 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: (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

The quaternary structure annotation of the template is used to model the target sequence in its oligomeric form. The method (Bertoni et al.) is based on a supervised machine learning algorithm, Support Vector Machines (SVM), which combines interface conservation, structural clustering, and other template features to provide a quaternary structure quality estimate (QSQE). The QSQE score is a number between 0 and 1, reflecting the expected accuracy of the interchain contacts for a model built based a given alignment and template. Higher numbers indicate higher reliability. This complements the GMQE score which estimates the accuracy of the tertiary structure of the resulting model.

References

BLAST
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L. BLAST+: architecture and applications. BMC Bioinformatics 10, 421-430 (2009).
HHblits
Remmert, M., Biegert, A., Hauser, A., Söding, J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 9, 173-175 (2012).

Table T1:

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

MRNSCFFNWLESKKTRGITMAEEKKANQLPDRSEVKAEDTWRLEDIFPSDEAWNKEFQAVKELIPNLSKYKGKLADSADHLYEALTYQDKVMERLGRLYT
YAHMRSDQDTGNSFYQGLNDKAGNLYTQAASATAYLVPEILSIEEDKLQQFILEKEELKLYSHAIEEITKERPHVLSEKEEALLAEASEVLGSSSNTFSV
LNNADITFPSIKDEDGNEKQITHGNFINFLESENREVRKNAFDAVYKTYGQYKNTMATTLSGTVKKDNFYARVKKYKSAREAALSNNSIPEEVYDNLVKT
INKHLPLLHRYIALRKKVLELDEVHIYDLYTPLVKDAGMKVTYEEAKDYMLKGLAPLGEEYASILKEGLENRWVDVYENKGKRNGAYSSGAYGTNPYILM
NWHNNVNNLFTLVHEFGHSVHSYYTRKHQPYPYGNYSIFVAEVASTTNEALLGEYLLNNLEDEKQRLYILNHMLEGFRGTVFRQTMFAEFEHLIHTKAQE
GEPLTPELLTKVYYDLNKKYFGDGMVIDKEIGLEWSRIPHFYYNYYVYQYATGYSAAQALSSQILKEGKPAVDRYIDFLKAGSSQYPIDVLKKAGVDMTS
PEPIEAACKMFEEKLDEMEELLMKVKQS

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
3ce2.1.A	37.16	monomer		HHblits	X-ray	2.60Å	0.39	0.94	Putative peptidase
3ce2.1.A	37.91	monomer		BLAST	X-ray	2.60Å	0.40	0.93	Putative peptidase
2qr4.1.A	52.09	homo-dimer	0.47	HHblits	X-ray	2.50Å	0.45	0.91	Peptidase M3B, oligoendopeptidase F
2qr4.1.A	52.14	homo-dimer	0.43	BLAST	X-ray	2.50Å	0.45	0.89	Peptidase M3B, oligoendopeptidase F
2qr4.1.B	52.09	homo-dimer	0.46	HHblits	X-ray	2.50Å	0.45	0.91	Peptidase M3B, oligoendopeptidase F
2qr4.1.B	52.14	homo-dimer	0.42	BLAST	X-ray	2.50Å	0.45	0.89	Peptidase M3B, oligoendopeptidase F
4ufb.3.A	14.20	monomer		HHblits	X-ray	1.80Å	0.27	0.82	ANGIOTENSIN-CONVERTING ENZYME
6f9t.1.A	14.88	monomer		HHblits	X-ray	1.60Å	0.28	0.80	Angiotensin-converting enzyme
3l3n.1.A	14.88	monomer		HHblits	X-ray	2.30Å	0.28	0.80	Angiotensin-converting enzyme
3sck.2.A	15.25	monomer		HHblits	X-ray	3.00Å	0.28	0.80	Angiotensin-converting enzyme 2 chimera
3nxq.1.A	14.20	monomer		HHblits	X-ray	1.99Å	0.27	0.82	Angiotensin-converting enzyme
3sck.1.A	15.25	monomer		HHblits	X-ray	3.00Å	0.28	0.80	Angiotensin-converting enzyme 2 chimera
2iux.1.A	14.88	monomer		HHblits	X-ray	2.80Å	0.28	0.80	ANGIOTENSIN-CONVERTING ENZYME
3d0h.1.A	15.02	monomer		HHblits	X-ray	3.10Å	0.28	0.81	Angiotensin-converting enzyme 2
3d0h.1.B	15.02	monomer		HHblits	X-ray	3.10Å	0.28	0.81	Angiotensin-converting enzyme 2
6f9v.1.A	14.40	monomer		HHblits	X-ray	1.69Å	0.27	0.82	Angiotensin-converting enzyme
3kbh.1.A	15.14	homo-dimer		HHblits	X-ray	3.31Å	0.28	0.80	Angiotensin-converting enzyme 2
2oc2.1.A	14.88	monomer		HHblits	X-ray	2.25Å	0.28	0.80	Angiotensin-converting enzyme, somatic isoform
5am8.1.A	14.40	monomer		HHblits	X-ray	1.90Å	0.27	0.82	ANGIOTENSIN-CONVERTING ENZYME
2c6f.1.A	14.26	monomer		HHblits	X-ray	3.01Å	0.27	0.82	ANGIOTENSIN-CONVERTING ENZYME, SOMATIC ISOFORM
5amc.1.A	14.40	monomer		HHblits	X-ray	1.65Å	0.27	0.82	ANGIOTENSIN-CONVERTING ENZYME
4apj.1.A	14.51	monomer		HHblits	X-ray	2.60Å	0.28	0.80	ANGIOTENSIN-CONVERTING ENZYME
1uze.1.A	14.51	monomer		HHblits	X-ray	1.82Å	0.28	0.80	ANGIOTENSIN CONVERTING ENZYME
4c2p.1.A	14.29	monomer		HHblits	X-ray	1.99Å	0.27	0.80	ANGIOTENSIN-CONVERTING ENZYME
2iul.1.A	14.48	monomer		HHblits	X-ray	2.01Å	0.28	0.80	ANGIOTENSIN-CONVERTING ENZYME
3sci.1.A	14.65	monomer		HHblits	X-ray	2.90Å	0.28	0.80	Angiotensin-converting enzyme 2
3sci.2.A	14.65	monomer		HHblits	X-ray	2.90Å	0.28	0.80	Angiotensin-converting enzyme 2
6cs2.1.D	15.54	monomer		HHblits	EM	NA	0.28	0.80	Angiotensin-converting enzyme 2
5a0p.1.A	16.67	monomer		HHblits	X-ray	1.40Å	0.29	0.16	ZINC METALLOPROTEASE ZMP1
5a0p.2.A	16.67	monomer		HHblits	X-ray	1.40Å	0.29	0.16	ZINC METALLOPROTEASE ZMP1
2n6j.1.A	16.67	monomer		HHblits	NMR	NA	0.29	0.16	Zinc metalloprotease Zmp1
4dv8.1.A	14.94	monomer		HHblits	X-ray	1.63Å	0.26	0.14	Lethal factor
5d1t.1.A	14.94	monomer		HHblits	X-ray	2.20Å	0.26	0.14	Lethal factor
4pkw.1.A	14.94	monomer		HHblits	X-ray	1.75Å	0.26	0.14	Lethal factor
4pks.1.A	14.94	monomer		HHblits	X-ray	2.30Å	0.26	0.14	Lethal factor
4wf6.1.A	14.94	monomer		HHblits	X-ray	2.65Å	0.26	0.14	Lethal factor
5d1s.1.A	14.94	monomer		HHblits	X-ray	2.10Å	0.26	0.14	Lethal factor
1yqy.1.A	14.94	monomer		HHblits	X-ray	2.30Å	0.26	0.14	Lethal factor
5a0r.1.A	14.81	monomer		HHblits	X-ray	1.25Å	0.29	0.13	ZINC METALLOPROTEASE ZMP1
5a0r.2.A	14.81	monomer		HHblits	X-ray	1.25Å	0.29	0.13	ZINC METALLOPROTEASE ZMP1
5a0s.1.A	14.81	monomer		HHblits	X-ray	2.56Å	0.29	0.13	ZINC METALLOPROTEASE ZMP1
5a0x.1.A	14.81	monomer		HHblits	X-ray	1.70Å	0.29	0.13	ZINC METALLOPROTEASE ZMP1

The table above shows the top 42 filtered templates. A further 324 templates were found which were considered to be less suitable for modelling than the filtered list.
4ger.1.A, 4wzv.1.A, 2rjp.3.A, 4auo.1.A, 1d7x.1.B, 1g9k.1.A, 2poj.1.A, 1y93.1.A, 1mnc.1.A, 1d7x.1.A, 2x93.1.A, 3dwc.1.A, 2jt5.1.A, 4i03.1.A, 1sat.1.A, 4c2o.1.A, 5l7f.2.A, 4g9l.1.A, 2o3e.1.A, 2h1n.1.A, 5uwn.4.A, 4m65.1.A, 1hv5.3.A, 3sks.1.A, 2mlr.1.A, 1ums.1.A, 2v4b.2.A, 2wo9.2.A, 3vtg.1.A, 5ue5.1.A, 5czw.1.A, 1d5j.1.A, 1gkd.1.A, 1esp.1.A, 4gwn.1.A, 3edg.1.A, 2xy9.1.A, 2kkm.1.A, 4h30.1.A, 4efs.1.A, 3dsl.1.A, 1qia.3.A, 4h2e.1.A, 3edh.1.A, 3shi.1.A, 1ztq.1.A, 1k7q.1.A, 2vqx.1.A, 2ow9.1.A, 1umt.1.A, 1rm8.1.A, 3o2x.5.A, 5lv0.1.A, 3o2x.5.B, 1go7.1.A, 3hb2.1.A, 1b3d.1.A, 1xud.2.A, 830c.1.A, 5n5k.1.A, 2clt.2.A, 1qia.4.A, 3tt4.1.A, 4qhi.2.B, 4qhi.2.A, 2krj.1.A, 2wo8.3.A, 1kuh.1.A, 3dpe.1.A, 1slm.1.A, 3ohl.1.A, 4qhi.1.A, 3nqz.1.B, 1kug.1.A, 4qhi.1.B, 2x91.1.A, 4h49.1.A, 4c2n.1.A, 1jiz.1.A, 1cgl.2.A, 1c3i.2.B, 1kui.1.A, 1go8.1.A, 3dbk.1.A, 1npc.1.A, 2ddy.1.A, 3ayk.1.A, 1c8t.1.B, 3lq0.1.A, 1jk3.1.A, 5l7f.1.A, 4imi.1.A, 1fbl.1.A, 3hdb.1.A, 3ma2.1.A, 3nqx.1.A, 2srt.1.A, 3uvc.1.A, 5uwl.1.A, 1uea.1.A, 2ow9.2.A, 3ahm.1.A, 1i1i.1.A, 3b2z.8.A, 2ydm.1.A, 1c3i.2.A, 2dw0.1.A, 2ero.1.B, 2ero.1.A, 1mmb.1.A, 1bqo.1.A, 1q3a.2.B, 1hv5.6.A, 3ljz.4.A, 2z2d.1.A, 2ayk.1.A, 3kry.3.A, 1mmp.1.A, 2erq.1.B, 2v4b.1.A, 1ros.1.A, 2w0d.2.A, 1bsw.1.A, 1bqb.1.A, 3hq2.1.A, 4h2e.2.A, 2ovx.1.A, 1ayk.1.A, 4bzs.1.A, 5tgw.1.A, 4h84.2.A, 3usn.1.A, 5vjc.1.A, 2rjp.1.A, 3kec.2.A, 3b2z.2.A, 3b2z.6.A, 1cqr.2.A, 4hx3.1.A, 3b2z.1.A, 1zp5.1.A, 1j36.1.A, 1g4k.3.A, 5fxn.1.A, 830c.2.A, 3ewj.2.A, 2dw0.2.A, 4ja1.2.A, 2a7g.1.A, 5uwn.1.A, 1ezm.1.A, 4k89.1.A, 1kbc.1.A, 5th9.3.C, 2ajf.1.A, 2jsd.1.A, 4r3v.1.A, 5uwk.2.A, 4ayk.1.A, 5i3m.1.A, 3c37.1.A, 5gwd.1.A, 1y79.1.A, 4fxy.1.A, 4on1.1.A, 3k7n.1.A, 3q2h.1.A, 4ygx.2.A, 1you.2.A, 1os9.1.A, 1hov.1.A, 3g5c.1.A, 2y6c.1.A, 1d5j.2.A, 2xyd.1.A, 4h30.1.B, 5uwl.2.A, 3q2h.2.A, 1fls.1.A, 2w0d.4.A, 1os2.3.A, 3o64.2.A, 3ba0.1.A, 3edi.1.A, 1k7i.1.A, 1os9.4.A, 3lea.1.A, 1g4k.1.A, 1qia.1.A, 3fxs.1.A, 4put.1.A, 2ddf.1.A, 1z3j.1.A, 5tgy.1.A, 1g4k.2.A, 2ozr.1.E, 2ddf.2.A, 2ozr.1.A, 1q3a.1.B, 1q3a.1.A, 4a7b.1.D, 1hv5.1.A, 1caq.1.A, 4ka7.1.A, 4a7b.1.C, 1hfs.1.A, 1ast.1.A, 1jao.1.A, 1ycm.1.A, 3kej.1.A, 3dng.1.A, 5i0l.2.A, 1cxv.1.A, 5czm.1.A, 5wvu.2.A, 1r4l.1.A, 5wvu.2.B, 1buv.1.A, 456c.1.B, 1d8m.1.A, 5a2r.1.A, 2rjq.1.A, 2ajf.2.A, 5giv.1.A, 5b5o.2.A, 1su3.2.A, 4h49.2.A, 1qib.1.A, 3f15.1.A, 1cgl.1.A, 5giv.3.B, 5h8x.1.A, 3tvc.1.A, 2k9c.1.A, 4r3v.2.A, 2cki.1.A, 4gwm.1.B, 4h84.1.A, 1gkc.1.A, 4gwm.1.A, 2k2g.1.A, 5h0u.1.A, 4il3.2.A, 1s4b.1.A, 3dti.1.A, 5ue4.2.A, 5a3y.1.A, 2w0d.1.A, 5uwk.1.A, 5e3x.1.A, 4gr8.1.A, 5l44.1.A, 3nqy.1.A, 2pjt.3.A, 1a85.1.A, 5b5o.1.A, 2dw1.2.A, 3hbu.1.A, 4c2r.1.A, 3o64.1.A, 4il3.1.A, 3ewj.1.A, 1k9x.2.A, 4ka8.1.A, 2o36.1.A, 1r42.1.A, 966c.1.A, 4jp4.1.B, 2n8r.1.A, 2d1n.1.A, 2dw2.1.A, 2d1o.1.A, 1bm6.1.A, 5uwn.3.A, 2erq.1.A, 3kry.1.A, 2mls.1.A, 2wo9.1.A, 1kap.1.A, 1utz.1.A, 1cgf.1.A, 2y6d.1.A, 2tcl.1.A, 3dsl.1.B, 5th6.1.A, 1ka4.1.A, 1usn.1.A, 1k7g.1.A, 1c8t.1.A, 2xs4.1.A, 2e2d.1.A, 4jp4.1.A, 3k7l.1.A, 5wvu.1.A, 1bzs.1.A, 3v96.1.B, 5ue2.1.A, 1cgf.2.A, 2jnp.1.A, 1eub.1.A, 1cge.1.A, 1bud.1.A, 2clt.1.A, 1qic.1.A, 1xud.1.A, 1fm1.1.A, 1uea.2.A, 1su3.1.A, 1d8m.2.A, 1hv5.2.A, 4k90.1.A, 4h3x.1.A, 3cqb.1.B, 3ayu.1.A, 3cqb.1.A, 3oho.1.A, 2pjt.1.A, 3hoa.1.A, 2ovx.2.A, 5ue3.1.A, 2e3x.1.A, 1you.1.A, 1oo9.1.A, 4xct.1.A