Workunit: P000002 Title:Protein analysis

Model Summary: Model information: Modelled residue range: Based on template: Sequence Identity [%]: Evalue: Quality information: QMEAN Z-Score: -0.721 1 to 103 1djrF (1.30 A) 100 2.07839e-46 Ligand information: Ligands in the template: BEZ: 3, GLA: 5, GOL: 3. Ligands in the model: none. Quaternary structure information: Template (1djr): PENTAMER Model: PENTAMER

Global Model Quality Estimation: QMEAN4 global scores: QMEANscore4: Estimated absolute model quality: Score components:

Local scores: Coloring by residue error: Residue error plot:

0.731

Z-Score: -0.721 QMEAN4 global scores: The QMEAN4 score is a composite score consisting of a linear combination of 4 statistical potential terms (estimated model reliability between 0-1). The pseudo-energies of the contributing terms are given below together with their Z-scores with respect to scores obtained for high-resolution experimental structures of similar size solved by X-ray crystallography: Scoring function term C_beta interaction energy All-atom pairwise energy Solvation energy Torsion angle energy Raw score -369.37 -19695.56 -64.26 -92.99 Z-score 1.38 0.94 0.56 -1.29

QMEAN4 score 0.731 -0.72 If you publish results from QMEAN, please cite the following paper: Benkert P, Biasini M, Schwede T. (2011). "Toward the estimation of the absolute quality of individual protein structure models." Bioinformatics, 27(3):343-50.

Local Model Quality Estimation:

Alignment:

TARGET 1djr_1 TARGET 1djr_1

1 1

APQTITEL CSEYRNTQIY TINDKILSYT ESMAGKREMV IITFKSGETF apqtitel cseyrntqiy tindkilsyt esmagkremv iitfksgetf hhhh hh hhhh hh sssss sss sssss sss ssss ssss ssss ssss ssss ssss ssss ssss sss sss

TARGET 1djr_1 TARGET 1djr_1

49 49

QVEVPGSQHI DSQKKAIERM KDTLRITYLT ETKIDKLCVW NNKTPNSIAA qvevpgsqhi dsqkkaierm kdtlritylt etkidklcvw nnktpnsiaa ss ss hhhhhhhhh hhhhhhhhhh hhhhhhhhh hhhhhhhhhh sssssss s sssssss s ssss ssss

TARGET 1djr_1 TARGET 1djr_1

99 99

ISMKN - AP QTITELCSEY RNTQIYTIND KILSYTESMA GKREMVIITF ismkn---ap qtitelcsey rntqiytind kilsytesma gkremviitf * sssss hhhhhh ssssssss ssssssss ssssssss sssss hhhhhh ssssssss ssssssss ssssssss

TARGET 1djr_1 TARGET 1djr_1

146 43

KSGETFQVEV PGSQHIDSQK KAIERMKDTL RITYLTETKI DKLCVWNNKT ksgetfqvev pgsqhidsqk kaiermkdtl rityltetki dklcvwnnkt sssss sssss hhh hhhhhhhhhh hhhhhh hhh hhhhhhhhhh hhhhhh s sssssss s sssssss

TARGET 1djr_1 TARGET 1djr_1

196 93

PNSIAAISMK - APQTITE pnsiaaismk ---apqtite * sssssss hhh sssssss hhh

LCSEYRNTQI YTINDKILSY TESMAGKREM lcseyrntqi ytindkilsy tesmagkrem hhh hhh ssss ssss ssss ssss ss sssss ss sssss sss sss

TARGET 1djr_1 TARGET 1djr_1

243 38

VIITFKSGET FQVEVPGSQH IDSQKKAIER MKDTLRITYL TETKIDKLCV viitfksget fqvevpgsqh idsqkkaier mkdtlrityl tetkidklcv sssss sssss ss sss ss sss hhhhhhhh hhhhhhhhhh h hhhhhhhh hhhhhhhhhh h ssssss ssssss

TARGET 1djr_1 TARGET 1djr_1

293 88

WNNKTPNSIA AISMKN - A PQTITELCSE YRNTQIYTIN DKILSYTESM wnnktpnsia aismkn---a pqtitelcse yrntqiytin dkilsytesm * ss sss ssssss hhhhhh ssssssss sssssss ss sss ssssss hhhhhh ssssssss sssssss

TARGET 1djr_1 TARGET 1djr_1

340 32

AGKREMVIIT FKSGETFQVE VPGSQHIDSQ KKAIERMKDT LRITYLTETK agkremviit fksgetfqve vpgsqhidsq kkaiermkdt lrityltetk s s sssssss s sssssss s sssss sssss hh hhhhhhhhhh hhhhhhh hh hhhhhhhhhh hhhhhhh

TARGET 1djr_1

390 82

IDKLCVWNNK TPNSIAAISM KN - APQTI TELCSEYRNT QIYTINDKIL idklcvwnnk tpnsiaaism kn---apqti telcseyrnt qiytindkil *

TARGET 1djr_1

ssssssss ssssssss

sssssss sssssss

h hhhhh h hhhhh

ss ssssss ss ssssss

TARGET 1djr_1 TARGET 1djr_1

437 26

SYTESMAGKR EMVIITFKSG ETFQVEVPGS QHIDSQKKAI ERMKDTLRIT sytesmagkr emviitfksg etfqvevpgs qhidsqkkai ermkdtlrit sssssss sssssss s sssssss s sssssss sssss sssss hhhhhh hhhhhhhhhh hhhhhh hhhhhhhhhh

TARGET 1djr_1 TARGET 1djr_1

487 76

YLTETKIDKL CVWNNKTPNS IAAISMKN yltetkidkl cvwnnktpns iaaismknhhh hhh ssss ssss ssss ssss s ssssssss s ssssssss

Modeling Log: 3.70 (SP3) Loading Template: 1djr_1.pdb Loading Raw Sequence Loading Alignment: ./NXXX.align.submit.fasta Removing HET groups from template structure Refining Raw Sequence Alignment ProModII: doing simple assignment of backbone ProModII: adding blocking groups Adding Missing Sidechains AddPolar H BuildDeletetedLoopsModel Optimizing Sidechains Adding Hydrogens Optimizing loops and OXT (nb = 5) Final Total Energy: -31993.855 KJ/mol Dumping Sequence Alignment

Template Selection Log: - Start SMR-Pipeline in automated mode on BC2-cluster at Tue Feb 14 06:41:32 2012

- Start BLAST for highly similar template structure identification - Blast template search was successfull, number of templates selected for modeling: - Send 1 target-template alignments for modeling - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ - ******************************************************************************** - 1djrF (1-103) is a 100% match - Workspace Pipeline parameter Cut-off parameters to model the target based on a BLAST target-template alignment Evalue : 0.0001 Minimum Template size (aa) for ranking : 25 Minimum Sequence identity : 60

1; entering modeling mo

Cut-off parameters to model the target based on a HHSearch target-template alignment Evalue : 0.0001 Probability : 50

MAC : Parameters for model selection Minimal number of uncovered target residues after BLAST to run HHSEARCH : Minimal number of uncovered target residues to model an additional template :

0.3

50 25

- Finish SMR-Pipeline in automated mode on BC2-cluster at Tue Feb 14 06:43:21 2012

Quaternary Structure Annotation of the Template 1djr is annotated as PENTAMER The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry The following biological unit was used to build the template structure: 1djr.pdb1.gz Quaternary Structure Modelling of the Target Protein The quaternary structure can be assumed to be identical To build the complex the following chains of the complex has been additionally identified: 1djrH 1djrD 1djrG 1djrE Model was succesfully built as PENTAMER. Ligand Modeling Log: Templates ligands section Ligands in the template: BEZ: 3, GLA: 5, GOL: 3. The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page. No ligands were included in the model. References: If you publish results using SWISS-MODEL, please cite the following papers: Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modeling. Bioinformatics, 22,195-201. Schwede T, Kopp J, Guex N, and Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Research 31: 3381-3385. Guex, N. and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18: 2714-2723.