Workunit: P000001 Title:ADH1

Model Summary:
Model information:
Modelled residue range:

2 to 348

Sequence Identity [%]:

Quaternary structure information:

2hcyB (2.44 A) Template (2hcy): TETRAMER
Model: TETRAMER
100

Evalue:

Based on template:

Ligand information:
Ligands in the template: 8ID: 2, ETF: 4, ZN: 8.
Ligands in the model: ZN: 5

Quality information:
QMEAN Z-Score: -0.588

Global Model Quality Estimation:

QMEAN4 global scores:
QMEANscore4:

Estimated absolute
model quality:

Local scores:
Score components:

Coloring by residue
error:

Residue error
plot:

0.72

Z-Score: -0.588
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

Raw score

Z-score

C_beta interaction energy

-78.12

-1.27

All-atom pairwise energy

-27184.73

-0.95

Solvation energy

-124.83

-0.27

Torsion angle energy

-349.66

-0.36

QMEAN4 score
0.720
-0.59
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
2hcy_1

1
1

SIPETQKG VIFYESHGKL EYKDIPVPKP KANELLINVK YSGVCHTDLH

sipetqkg vifyeshgkl eykdipvpkp kanellinvk ysgvchtdlh

TARGET
2hcy_1

TARGET
2hcy_1

ss s
ss s

49
49

TARGET
2hcy_1

TARGET
2hcy_1

99
99

TARGET
2hcy_1

TARGET
2hcy_1

199
199

TARGET
2hcy_1

TARGET
2hcy_1

299
299

348
1

396
49

ssss sssss
ssss sssss

ss s
ss s

hhhh
hhhh

sssssss
sssssss

hhhhhhhh hhhhh
hhhhhhhh hhhhh

sss
sss

GIDGGEGKEE LFRSIGGEVF IDFTKEKDIV GAVLKATDGG AHGVINVSVS

gidggegkee lfrsiggevf idftkekdiv gavlkatdgg ahgvinvsvs
hhh hhhh
hhh hhhh

ss sss
ss sss

hh hhhhhh
hh hhhhhh

ssssss
ssssss

EAAIEASTRY VRANGTTVLV GMPAGAKCCS DVFNQVVKSI SIVGSYVGNR

eaaieastry vrangttvlv gmpagakccs dvfnqvvksi sivgsyvgnr
ssssss
sssss

sssss sshhhhhh s sssss

sssss sshhhhhh s sssss

h
h

ADTREALDFF ARGLVKSPIK VVGLSTLPEI YEKMEKGQIV GRYVVDTSK

adtrealdff arglvkspik vvglstlpei yekmekgqiv gryvvdtskhhhhhhhhhh hh
hhhhhhhhhh hh

TARGET
2hcy_1

TARGET
2hcy_1

hhhh hhhhhh
hhhh hhhhhh

hhhhhhhh
hhhhhhhh

TARGET
2hcy_1

TARGET
2hcy_1

sss
sss

APILCAGITV YKALKSANLM AGHWVAISGA AGGLGSLAVQ YAKAMGYRVL

apilcagitv ykalksanlm aghwvaisga agglgslavq yakamgyrvl

sss
sss

249
249

sss ss sss
sss ss sss

ACEYCELGNE SNCPHADLSG YTHDGSFQQY ATADAVQAAH IPQGTDLAQV

aceycelgne sncphadlsg ythdgsfqqy atadavqaah ipqgtdlaqv

hhh
hhh

TARGET
2hcy_1

TARGET
2hcy_1

ss ssssssssss
ss ssssssssss

hhhhh
hhhhh

149
149

hhhh
hhhh

AWHGDWPLPV KLPLVGGHEG AGVVVGMGEN VKGWKIGDYA GIKWLNGSCM

awhgdwplpv klplvggheg agvvvgmgen vkgwkigdya gikwlngscm
hhh
hhh

TARGET
2hcy_1

TARGET
2hcy_1

sssssssss ssss
sssssssss ssss

- SIPETQKG
--sipetqkg
*
sssss
sssss

sss ssss
sss ssss

hhhh hhhhh
hhh hhhhh

ssssss
ssssss

VIFYESHGKL EYKDIPVPKP KANELLINVK YSGVCHTDLH

vifyeshgkl eykdipvpkp kanellinvk ysgvchtdlh
ss
ss

sssssss
sssssss

sssssssss ssss
sssssssss ssss

hhhh
hhhh

AWHGDWPLPV KLPLVGGHEG AGVVVGMGEN VKGWKIGDYA GIKWLNGSCM

awhgdwplpv klplvggheg agvvvgmgen vkgwkigdya gikwlngscm

TARGET
2hcy_1

TARGET
2hcy_1

hhh
hhh

446
99

TARGET
2hcy_1

TARGET
2hcy_1

496
149

TARGET
2hcy_1

TARGET
2hcy_1
TARGET
2hcy_1

TARGET
2hcy_1
TARGET
2hcy_1

TARGET
2hcy_1
TARGET
2hcy_1

TARGET
2hcy_1

743
49

TARGET
2hcy_1

TARGET
2hcy_1

793
99

sss
sss

hhh hhh
hhh hhh

ss sss
ss sss

hh hhhhhhh
hh hhhhhhh

sssss
sssss

sssss
sssss

sssss sshhhhhh s sssss

sssss sshhhhhh s sssss

h
h

ADTREALDFF ARGLVKSPIK VVGLSTLPEI YEKMEKGQIV GRYVVDTSK

adtrealdff arglvkspik vvglstlpei yekmekgqiv gryvvdtsk-

- SIPETQKG
--sipetqkg
*
ss
ss

s ssss
s ssss

hhh hhhh
hhh hhhh

ssssss
ssssss

VIFYESHGKL EYKDIPVPKP KANELLINVK YSGVCHTDLH

vifyeshgkl eykdipvpkp kanellinvk ysgvchtdlh
s
s

sssssssss ssss
sssssssss ssss

hhhh
hhhh

AWHGDWPLPV KLPLVGGHEG AGVVVGMGEN VKGWKIGDYA GIKWLNGSCM

awhgdwplpv klplvggheg agvvvgmgen vkgwkigdya gikwlngscm
ss ssssssssss
ss ssssssssss

sss ss sss
sss ss sss

ACEYCELGNE SNCPHADLSG YTHDGSFQQY ATADAVQAAH IPQGTDLAQV

aceycelgne sncphadlsg ythdgsfqqy atadavqaah ipqgtdlaqv
hhhhh
hhhhh

843
149

hhhhhh hhhhh
hhhhhh hhhhh

EAAIEASTRY VRANGTTVLV GMPAGAKCCS DVFNQVVKSI SIVGSYVGNR

eaaieastry vrangttvlv gmpagakccs dvfnqvvksi sivgsyvgnr

hhh
hhh

TARGET
2hcy_1

TARGET
2hcy_1

sssssss
sssssss

hhhhhhhhhh h
hhhhhhhhhh h

695
1

hhhh
hhhh

ss s

GIDGGEGKEE LFRSIGGEVF IDFTKEKDIV GAVLKATDGG AHGVINVSVS

gidggegkee lfrsiggevf idftkekdiv gavlkatdgg ahgvinvsvs

hhhhhhh
hhhhhhh

646
299

ssss sssss
ssss sssss

hhhh hhhhhh
hhhhh hhhhhh

sss
sss

596
249

sss
sss

APILCAGITV YKALKSANLM AGHWVAISGA AGGLGSLAVQ YAKAMGYRVL

apilcagitv ykalksanlm aghwvaisga agglgslavq yakamgyrvl
hhh
hh

546
199

sss ss sss
sss ss sss

ACEYCELGNE SNCPHADLSG YTHDGSFQQY ATADAVQAAH IPQGTDLAQV

aceycelgne sncphadlsg ythdgsfqqy atadavqaah ipqgtdlaqv
hhhh
hhhh

TARGET
2hcy_1

TARGET
2hcy_1

ss ssssssssss
ss ssssssssss

sss
sss

ssss sssss
ssss sssss

ss s
ss s

hhhh
hhhh

APILCAGITV YKALKSANLM AGHWVAISGA AGGLGSLAVQ YAKAMGYRVL

apilcagitv ykalksanlm aghwvaisga agglgslavq yakamgyrvl

TARGET
2hcy_1

TARGET
2hcy_1

hhh
hhh

893
199

TARGET
2hcy_1

TARGET
2hcy_1

943
249

TARGET
2hcy_1

TARGET
2hcy_1

1042
1

1090
49

TARGET
2hcy_1

TARGET
2hcy_1

1140
99

TARGET
2hcy_1

TARGET
2hcy_1

1240
199

- SIPETQKG
--sipetqkg
*
sssss
sssss

hh hhhhhh
hh hhhhhh

ssssss
ssssss

sssss sshhhhhh s sssss

sssss sshhhhhh s sssss

h
h

sss ssss
sss ssss

hhhh hhhhh
hhh hhhhh

ssssss
ssssss

VIFYESHGKL EYKDIPVPKP KANELLINVK YSGVCHTDLH

vifyeshgkl eykdipvpkp kanellinvk ysgvchtdlh
ss
ss

sssssss
sssssss

sssssssss ssss
sssssssss ssss

hhhh
hhhh

AWHGDWPLPV KLPLVGGHEG AGVVVGMGEN VKGWKIGDYA GIKWLNGSCM

awhgdwplpv klplvggheg agvvvgmgen vkgwkigdya gikwlngscm
ss ssssssssss
ss ssssssssss

sss ss sss
sss ss sss

ACEYCELGNE SNCPHADLSG YTHDGSFQQY ATADAVQAAH IPQGTDLAQV

aceycelgne sncphadlsg ythdgsfqqy atadavqaah ipqgtdlaqv
sss
sss

ssss sssss
ssss sssss

hhhh
hhhh

ss s

APILCAGITV YKALKSANLM AGHWVAISGA AGGLGSLAVQ YAKAMGYRVL

apilcagitv ykalksanlm aghwvaisga agglgslavq yakamgyrvl
hhhh hhhhhh
hhhhh hhhhhh

sssssss
sssssss

hhhhhh hhhhh
hhhhhh hhhhh

sss
sss

GIDGGEGKEE LFRSIGGEVF IDFTKEKDIV GAVLKATDGG AHGVINVSVS

gidggegkee lfrsiggevf idftkekdiv gavlkatdgg ahgvinvsvs
sss
sss

1290

sss
sss

ADTREALDFF ARGLVKSPIK VVGLSTLPEI YEKMEKGQIV GRYVVDTSK

adtrealdff arglvkspik vvglstlpei yekmekgqiv gryvvdtsk-

hhh
hh

TARGET
2hcy_1

TARGET

ssssss
sssss

hhhh
hhhh

1190
149

hhhhhhhh hhhhh
hhhhhhhh hhhhh

EAAIEASTRY VRANGTTVLV GMPAGAKCCS DVFNQVVKSI SIVGSYVGNR

eaaieastry vrangttvlv gmpagakccs dvfnqvvksi sivgsyvgnr

hhh
hhh

TARGET
2hcy_1

TARGET
2hcy_1

ss sss
ss sss

hhhhhhhhhh hh
hhhhhhhhhh hh

TARGET
2hcy_1

TARGET
2hcy_1

hhh hhhh
hhh hhhh

hhhhhhhh
hhhhhhhh

993
299

sssssss
sssssss

GIDGGEGKEE LFRSIGGEVF IDFTKEKDIV GAVLKATDGG AHGVINVSVS

gidggegkee lfrsiggevf idftkekdiv gavlkatdgg ahgvinvsvs
sss
sss

TARGET
2hcy_1

TARGET
2hcy_1

hhhh hhhhhh
hhhh hhhhhh

hhh hhh
hhh hhh

ss sss
ss sss

hh hhhhhhh
hh hhhhhhh

sssss
sssss

EAAIEASTRY VRANGTTVLV GMPAGAKCCS DVFNQVVKSI SIVGSYVGNR

2hcy_1

249

TARGET
2hcy_1

TARGET
2hcy_1

eaaieastry vrangttvlv gmpagakccs dvfnqvvksi sivgsyvgnr

hhhhhhh
hhhhhhh

1340
299

TARGET
2hcy_1

sssss
sssss

sssss sshhhhhh s sssss

sssss sshhhhhh s sssss

h
h

ADTREALDFF ARGLVKSPIK VVGLSTLPEI YEKMEKGQIV GRYVVDTSK

adtrealdff arglvkspik vvglstlpei yekmekgqiv gryvvdtskhhhhhhhhhh h
hhhhhhhhhh h

s ssss
s ssss

hhh hhhh
hhh hhhh

ssssss
ssssss

Modeling Log:
3.70 (SP3)
Loading Template: 2hcy_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:
-51857.605 KJ/mol
Dumping Sequence Alignment

Template Selection Log:

- Start SMR-Pipeline in automated mode on BC2-cluster at Tue Nov 19 15:33:19 2013

- Start BLAST for highly similar template structure identification

- Blast template search was successfull, number of templates selected for modeling:

1; entering modeling mo

- Send 1 target-template alignments for modeling

-

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
********************************************************************************
2hcyB (2-348) 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
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

50

residues to model an additional template :

25

- Finish SMR-Pipeline in automated mode on BC2-cluster at Tue Nov 19 15:42:26 2013

Quaternary Structure Annotation of the Template

2hcy 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: 2hcy.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: 2hcyA
Model was succesfully built as TETRAMER.
Ligand Modeling Log: Templates ligands section
Ligands in the template: 8ID: 2, ETF: 4, ZN: 8.
Ligands in the template that will be assessed: ZN1, ZN2, ZN33, ZN34, ZN61, ZN62, ZN93, ZN94.
Models ligands section
ZN1
One or more ligands atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other
ligands.
Given the properties calculated previously, the ligand z.ZN1 will not be included in the final model.
ZN1: conservation:True, RMSD:False, included: False
ZN2
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is lesser than two: 0.030
Given the properties calculated previously, the ligand z.ZN2 will be included in the final model.
ZN2: conservation:True, RMSD:True, included: True
ZN33
One or more ligands atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other
ligands.
Given the properties calculated previously, the ligand z.ZN33 will not be included in the final model.
ZN33: conservation:True, RMSD:False, included: False
ZN34
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is lesser than two: 0.120
Given the properties calculated previously, the ligand z.ZN34 will be included in the final model.
ZN34: conservation:True, RMSD:True, included: True
ZN61
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is lesser than two: 1.510
Given the properties calculated previously, the ligand z.ZN61 will be included in the final model.
ZN61: conservation:True, RMSD:True, included: True
ZN62
One or more ligands atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other
ligands.
Given the properties calculated previously, the ligand z.ZN62 will not be included in the final model.
ZN62: conservation:True, RMSD:False, included: False
ZN93
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is lesser than two: 0.040
Given the properties calculated previously, the ligand z.ZN93 will be included in the final model.
ZN93: conservation:True, RMSD:True, included: True
ZN94
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is lesser than two: 0.020
Given the properties calculated previously, the ligand z.ZN94 will be included in the final model.

ZN94: conservation:True, RMSD:True, included: True

The new model with the included ligands was saved successfully.
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.