Workunit: P000004 Title:

Model Summary: Model information: Modelled residue range: Based on template: Sequence Identity [%]: Evalue: Quality information: QMEAN Z-Score: -1.677 13 to 240 Quaternary structure information: 2y3pB (2.62 A) Template (2y3p): TETRAMER Model: TETRAMER 100 9.11196e-131 Ligand information: Ligands in the template: MG: 8, SM8: 4. Ligands in the model: none.

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

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

0.661

Z-Score: -1.677 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 -184.44 -12487.19 -21.59 -233.07 Z-score -0.29 -1.09 -2.42 -0.18

QMEAN4 score 0.661 -1.68 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 2y3p_1 TARGET 2y3p_1

1 23

DYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV dyamsviv gralpdvrdg lkpvhrrvly amnvlgndwn kaykksarvv hhhhhh hh hhhhhh hhh hhhhhhhh hhhhh hhhhhhhh hhhhh ssshhhh ssshhhh

TARGET 2y3p_1 TARGET 2y3p_1

49 71

GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY MLVDGQGNFG SIDGDSAAAM gdvigkyhph gdsavydtiv rmaqpfslry mlvdgqgnfg sidgdsaaam hhhhhh hhhhhh hhhhhhh hhh hhhhhhh hhh sssss sssss

TARGET 2y3p_1 TARGET 2y3p_1

99 121

RYTEIRLAKI AHELMADLEK ETVDFVDNYD GTEKIPDVMP TKIPNLLVNG ryteirlaki ahelmadlek etvdfvdnyd gtekipdvmp tkipnllvng ssssss h hhhh ssssss h hhhh sssss sssss sssss sssss hhhhh hhhhh

TARGET 2y3p_1 TARGET 2y3p_1

149 171

SSGIAVGMAT NIPPHNLTEV INGCLAYIDD EDISIEGLME HIPGPDFPTA ssgiavgmat nipphnltev ingclayidd edisieglme hipgpdfpta sss sss s ss s ss hhhh hhhhhhhhh hhhh hhhhhhhhh hhhh hhh

TARGET 2y3p_1 TARGET 2y3p_1

199 221

AIINGRRGIE EAYRTGRGKV --------- ---------- ---------aiingrrgie eayrtgrgkv -yiraraeve vdaktgreti ivheipyqvn hhhh hhhh hhhh hhhh sssss

ssss

sssssssss ss

ssss sss

TARGET 2y3p_1 TARGET 2y3p_1

270

---------- ---------- ---------- ---------- ---------karliekiae lvkekrvegi salrdesdkd gmrivievkr davgevvlnn

hhhhhhhhhh hhh

ss ssssssss

sssssssss

hhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

320

---------- ---------- ---------- ---------- ---------lysqtqlqvs fginmvalhh gqpkimnlkd iiaafvrhrr evvtrrtife

hhh

ssss sssssssss

sssss hhh hhhhhhhhhh hhhhhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

370

---------- ---------- ---------- ---------- ---------lrkardrahi lealavalan idpiielirh aptpaeakta lvanpwqlgn

hhhhhhhhhh hhhhhhh

hhhhhhhhh

hhhhhhh hh

TARGET 2y3p_1

420

---------- ---------- ---------- ---------- ---------vaamledaar pewlepefgv rdglyylteq qaqaildlrl qkltglehek

TARGET 2y3p_1

hhhhh

ss s

sss

hh hhhhhhh

hh

hhhhh

TARGET 2y3p_1 TARGET 2y3p_1

474

---------- ---------- ---------- ---------- ---------lldeykelld qiaellrilg sadrlmevir eelelvreqf gdkrrteit* hhhhhhhhhh hhhhhhhh hhhhhhhhh hhhhhhhhh sss

TARGET 2y3p_1 TARGET 2y3p_1

219 13

IEEELKSSY LDYAMSVIVG RALPDVRDGL KPVHRRVLYA MNVLGNDWNK -ieeelkssy ldyamsvivg ralpdvrdgl kpvhrrvlya mnvlgndwnk hh hh hhhhhhhh hh hhhhhhhh hh hhhhhhhhh hhhh hhhhhhhhh hhhh

TARGET 2y3p_1 TARGET 2y3p_1

268 62

AYKKSARVVG DVIGKYHPHG DSAVYDTIVR MAQPFSLRYM LVDGQGNFGS aykksarvvg dvigkyhphg dsavydtivr maqpfslrym lvdgqgnfgs ssshhhhh hhhh ssshhhhh hhhhh hhhhhhhh hh hhhhhhhh hh sssss sssss

TARGET 2y3p_1 TARGET 2y3p_1

318 112

IDGDSAAAMR YTEIRLAKIA HELMADLEKE TVDFVDNYDG TEKIPDVMPT idgdsaaamr yteirlakia helmadleke tvdfvdnydg tekipdvmpt ssssss hh hhh ssssss hh hhh sssss sssss sssss sssss

TARGET 2y3p_1 TARGET 2y3p_1

368 162

KIPNLLVNGS SGIAVGMATN IPPHNLTEVI NGCLAYIDDE DISIEGLMEH kipnllvngs sgiavgmatn ipphnltevi ngclayidde disieglmeh hhhhh s ssss hhhhh s ssss ssss s ssss s hhhhh hhhhhhhh hhhhh hhhhhhhh hhhhhhh hhh h

TARGET 2y3p_1 TARGET 2y3p_1

418 212

IPGPDFPTAA IINGRRGIEE AYRTGRGKV ---------- ---------ipgpdfptaa iingrrgiee ayrtgrgkv- yiraraevev daktgretii hhhhh hhh hhhhh hhh sssss

s sss

ssssssssss s

sssss

TARGET 2y3p_1 TARGET 2y3p_1

261

---------- ---------- ---------- ---------- ---------vheipyqvnk arliekiael vkekrvegis alrdesdkdg mrivievkrd

ss

h hhhhhhhhhh hhh

sss sssssss

s ssssssss

TARGET 2y3p_1 TARGET 2y3p_1

311

---------- ---------- ---------- ---------- ---------avgevvlnnl ysqtqlqvsf ginmvalhhg qpkimnlkdi iaafvrhrre

hhhhhhhh hhh

sssss ssssssss

sssss hhhh hhhhhhhhhh

TARGET 2y3p_1

361

---------- ---------- ---------- ---------- ---------vvtrrtifel rkardrahil ealavalani dpiielirha ptpaeaktal

TARGET 2y3p_1

hhhhhhhhhh hhhhhhhhhh hhhhhhh

hhhhhhhhh

hhhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

411

---------- ---------- ---------- ---------- ---------vanpwqlgnv aamledaarp ewlepefgvr dglyylteqq aqaildlrlq

h hhh

sss

sss

hhh hhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

465

---------- ---------- ---------- ---------- ---------kltglehekl ldeykelldq iaellrilgs adrlmevire elelvreqfg

hhhh hhhhhhhhhh hhhhhhhh

hhhhhhhhh hhhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

447 515

--------- DYAMSVIVGR ALPDVRDGLK dkrrteit-- dyamsvivgr alpdvrdglk * hhhhhhhh sss hhhhhhhh h

PVHRRVLYAM NVLGNDWNKA pvhrrvlyam nvlgndwnka hhhhhhhhhh hhh hhhhhhhhhh hhh

TARGET 2y3p_1 TARGET 2y3p_1

487 63

YKKSARVVGD VIGKYHPHGD SAVYDTIVRM AQPFSLRYML VDGQGNFGSI ykksarvvgd vigkyhphgd savydtivrm aqpfslryml vdgqgnfgsi ssshhhhhh hhhh ssshhhhhh hhhh hhhhhhhhh h hhhhhhhhh h s ssss s ssss

TARGET 2y3p_1 TARGET 2y3p_1

537 113

DGDSAAAMRY TEIRLAKIAH ELMADLEKET VDFVDNYDGT EKIPDVMPTK dgdsaaamry teirlakiah elmadleket vdfvdnydgt ekipdvmptk ssssss hhh hh ssssss hhh hh sssss sssss sssss sssss

TARGET 2y3p_1 TARGET 2y3p_1

587 163

IPNLLVNGSS GIAVGMATNI PPHNLTEVIN GCLAYIDDED ISIEGLMEHI ipnllvngss giavgmatni pphnltevin gclayidded isieglmehi hhhhh ss s hhhhh ss s sss sss hhhhhh hhhhhhh hhhhhh hhhhhhh hhhh hhh

TARGET 2y3p_1 TARGET 2y3p_1

637 213

PGPDFPTAAI INGRRGIEEA YRTGRGKV - ---------- ---------pgpdfptaai ingrrgieea yrtgrgkv-y iraraevevd aktgretiiv hhhhhh hh hhhhhh hh sssss s ssssssssss

ss ss

ssssss

TARGET 2y3p_1 TARGET 2y3p_1

262

---------- ---------- ---------- ---------- ---------heipyqvnka rliekiaelv kekrvegisa lrdesdkdgm rivievkrda

hh hhhhhhhhhh h

ssss ssssss

ss sssssss

TARGET

---------- ---------- ---------- ---------- ----------

2y3p_1 TARGET 2y3p_1

312

vgevvlnnly sqtqlqvsfg inmvalhhgq pkimnlkdii aafvrhrrev

hhhhhhhhh h

ssssss sssssss

s ssss hhhhh hhhhhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

362

---------- ---------- ---------- ---------- ---------vtrrtifelr kardrahile alavalanid piielirhap tpaeaktalv

hhhhhhhhhh hhhhhhhhhh hhhhh

hh hhhhhhh

hhhhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

412

---------- ---------- ---------- ---------- ---------anpwqlgnva amledaarpe wlepefgvrd glyylteqqa qaildlrlqk

hh hhh

sss

sss

hhhh hhhhh

hh

TARGET 2y3p_1 TARGET 2y3p_1

466

---------- ---------- ---------- ---------- ---------ltglehekll deykelldqi aellrilgsa drlmeviree lelvreqfgd

hhhhhhh hhhhhhhhhh hhhhhh

h hhhhhhhhhh hhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

665 516

-------- I EEELKSSYLD YAMSVIVGRA LPDVRDGLKP VHRRVLYAMN krrteit--i eeelkssyld yamsvivgra lpdvrdglkp vhrrvlyamn * hh hhhhhhhhhh h hhhhhhhhhh sss hh hhhhhhhhhh h hhhhhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

706 54

VLGNDWNKAY KKSARVVGDV IGKYHPHGDS AVYDTIVRMA QPFSLRYMLV vlgndwnkay kksarvvgdv igkyhphgds avydtivrma qpfslrymlv hh hh ssshhhhhhh hh ssshhhhhhh hhh hhhhhhhhhh hhhhhhhhhh ss ss

TARGET 2y3p_1 TARGET 2y3p_1

756 104

DGQGNFGSID GDSAAAMRYT EIRLAKIAHE LMADLEKETV DFVDNYDGTE dgqgnfgsid gdsaaamryt eirlakiahe lmadleketv dfvdnydgte sss sss s sssss hhhh h s sssss hhhh h sssss sssss s s

TARGET 2y3p_1 TARGET 2y3p_1

806 154

KIPDVMPTKI PNLLVNGSSG IAVGMATNIP PHNLTEVING CLAYIDDEDI kipdvmptki pnllvngssg iavgmatnip phnlteving clayiddedi ssss ssss hhhhh sss ss hhhhh sss ss sssss sssss hhhhhhh hhhhhh hhhhhhh hhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

856 204

SIEGLMEHIP GPDFPTAAII NGRRGIEEAY RTGRGKV -- ---------sieglmehip gpdfptaaii ngrrgieeay rtgrgkvyir araevevdak hhhhhhh hhh h hhhhhhh h hhhhhhh h ssssssss ssssssss

sss s

TARGET 2y3p_1 TARGET 2y3p_1

254

---------- ---------- ---------- ---------- ---------tgretiivhe ipyqvnkarl iekiaelvke krvegisalr desdkdgmri

sssssss

hhhh hhhhhhhhhh

ssssss ssss

ssss

TARGET 2y3p_1 TARGET 2y3p_1

304

---------- ---------- ---------- ---------- ---------vievkrdavg evvlnnlysq tqlqvsfgin mvalhhgqpk imnlkdiiaa

sssss

h hhhhhhhhhh

ssssssss sssss

sss ss hhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

354

---------- ---------- ---------- ---------- ---------fvrhrrevvt rrtifelrka rdrahileal avalanidpi ielirhaptp

hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhh

hhh hhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

404

---------- ---------- ---------- ---------- ---------aeaktalvan pwqlgnvaam ledaarpewl epefgvrdgl yylteqqaqa

hhhhhhhh

hhhh

sss

s ss

hhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

458

---------- ---------- ---------- ---------- ---------ildlrlqklt glehekllde ykelldqiae llrilgsadr lmevireele

hhh

hhhhhhh hhhhhhhhhh hhhhh

hh hhhhhhhhhh

TARGET 2y3p_1 TARGET 2y3p_1

508

---------- ----lvreqfgdkr rteit

hhhhh

sss

Modeling Log: 3.70 (SP3) Loading Template: 2y3p_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 = 4) Final Total Energy: -39869.016 KJ/mol Dumping Sequence Alignment

Template Selection Log: - Start SMR-Pipeline in automated mode on BC2-cluster at Fri Feb 14 15:04:27 2014

- 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 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ **************************************************************************** - 2y3pB (13-240) 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 : 0.3 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 :

50 25

- Finish SMR-Pipeline in automated mode on BC2-cluster at Fri Feb 14 15:07:51 2014

Quaternary Structure Annotation of the Template 2y3p is annotated as TETRAMER 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: 2y3p.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: 2y3pA Model was succesfully built as TETRAMER. Ligand Modeling Log: Templates ligands section Ligands in the template: MG: 8, SM8: 4. Ligands in the template that will be assessed: MG1, MG103, MG104, MG152, MG153, MG2, MG50, MG51. Models ligands section MG1 The ligand is farther than 3 Angstroem from the template, so it is assumed that they are not interacting. Given the properties calculated previously, the ligand z.MG1 will not be included in the final model. MG1: conservation:False, RMSD:False, included: False MG2 The ligand is farther than 3 Angstroem from the template, so it is assumed that they are not interacting. Given the properties calculated previously, the ligand z.MG2 will not be included in the final model. MG2: conservation:False, RMSD:False, included: False MG50 The ligand is farther than 3 Angstroem from the template, so it is assumed that they are not interacting. Given the properties calculated previously, the ligand z.MG50 will not be included in the final model. MG50: conservation:False, RMSD:False, included: False

MG51 The ligand is farther than 3 Angstroem from the template, so it is assumed that they are not interacting. Given the properties calculated previously, the ligand z.MG51 will not be included in the final model. MG51: conservation:False, RMSD:False, included: False MG103 The ligand is farther than 3 Angstroem from the template, so it is assumed that they are not interacting. Given the properties calculated previously, the ligand z.MG103 will not be included in the final model. MG103: conservation:False, RMSD:False, included: False MG104 The ligand is farther than 3 Angstroem from the template, so it is assumed that they are not interacting. Given the properties calculated previously, the ligand z.MG104 will not be included in the final model. MG104: conservation:False, RMSD:False, included: False MG152 The ligand is farther than 3 Angstroem from the template, so it is assumed that they are not interacting. Given the properties calculated previously, the ligand z.MG152 will not be included in the final model. MG152: conservation:False, RMSD:False, included: False MG153 The ligand is farther than 3 Angstroem from the template, so it is assumed that they are not interacting. Given the properties calculated previously, the ligand z.MG153 will not be included in the final model. MG153: conservation:False, RMSD:False, included: False 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.