Workunit: P000010 Title:W

Model Summary:
Model information:
Modelled residue range:

1 to 228

Based on template:

4anjA (2.60 A)
Remark: No search
for template was
performed.
Only user specified
template was used
for modelling.

Quaternary structure information:

Sequence Identity [%]:

96.93

Evalue:

9.86566e-131

Ligands in the template: ADP: 1, ALA: 1, ALF: 1,

MG: 1.
Ligands in the model: none.

Template (4anj): HETERO DIMER

Model built :SINGLE CHAIN
Ligand information:

Quality information:
QMEAN Z-Score: -0.907

Global Model Quality Estimation:

QMEAN4 global scores:
QMEANscore4:

Estimated absolute
model quality:

Local scores:
Score components:

Coloring by residue
error:

Residue error
plot:

0.725

Z-Score: -0.907
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

-60.00

-1.64

All-atom pairwise energy

-4413.35

-1.78

Solvation energy

-26.26

0.29

Torsion angle energy

-52.94

-0.68

QMEAN4 score
0.725
-0.91
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:

4anjA

4anjA

4anjA

sssss

58

4anjA

4anjA

gkpvwaphpt dgfqvgnivd igpdsltiep lktflalinq vfpaeedskk

sssssssss ss sssssss s

dvedncslmy lneatllhni kvryskdriy tyvaniliav npyfdipkiy

hhhhhhhh hhhh

108

sssss

ss sss

sssss s

ssetiksyqg kslgtmpphv faiadkafrd mkvlklsqsi ivsgesgagk

4anjA

4anjA

hhhhhh

158

4anjA

4anjA

211

4anjA

4anjA

4anjA

4anjA

368

431

4anjA

4anjA

4anjA

hhhh

hhhhh

hhhh

hhh hh

hhhhhhhhhh hhhhhhhh

sss

sss

stqaleycae llgldqddlr vslttrvkvp lkveqannar dalaktvysh

hhhhh hhhh

hhhhhhhh hhhhhhhhhh

lfdhvvnrvn qcfpfetssy figvldiagf eyfehnsfeq fcinycnekl

s ssssss

hhh hhhhhhhhhh

qqffnerilk eeqelyqkeg lgvnevhyvd nqdcidliea rlvgildild

hhhhhhhhhh hhhhhhhhh

531

hhhh hhh

lddhgdfirm ctamkkigld deekldlfrv vagvlhlgni dfeecnlknk

hhhhhhhhhh h

481

sss ssss

erlhlsspdn frylnrgctr yfanketdkq ilqnrkspey lkagslkdpl

hhhhhhhhh hh

4anjA

4anjA

ss ssssssss

hhhhhhhh hhhhhhh

4anjA

4anjA

h hhhhhhhhhh hhsss

hhh

311

eihfnekssv vggfvshyll eksricvqgk eernyhifyr lcagasedir

sssss

261

ssss sss

tentkfvlry ltesygtidd riveanplle afgnaktvrn nnssrfgkfv

hhhhhhhhhh hhhh

4anjA

4anjA

hhhhhhhhhh hhhh

hhhhhhhh

hhhhhh

eenrlpqpsd qhftsavhqk hkdhfrlsip rksklaihrn irddegfiir

hhhh

h hhhhhhhhh

sss

ssssss

4anjA

581

4anjA

4anjA

647

4anjA

4anjA

697

747

1
797

29
1029

79
1079

TARGET
4anjA

TARGET
4anjA
TARGET
4anjA

hh

hhhhhh hhhhh

hhhh hhhh

hhh hhhhhhhhhh hhhhhhhhhh

MSKGEELF TGVVPILVEL DGDVNGHKFS

qwcslsvikl knkikyraea --vskgeelf tgvvpilvel dgdvnghkfs
hhhhh
hhhhhh

sssssss sssss ssss

sssssss sssss ssss

VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTFSYGV QCFSRYPDHM

vsgegegdat ygkltlkfic ttgklpvpwp tlvttf---v qcfarypdhm
sssssssss s
sssssssss s

hhhh
hhh

hh
hh

KQHDFFKSAM PEGYVQERTI FFKDDGNYKT RAEVKFEGDT LVNRIELKGI

rqhdffksam pegyvqerti ffkddgnykt raevkfegdt lvnrielkgi
hhh
hhh

ssssssss sss
ssssssss sss

sssss sssssss
sssss sssssss

s ssssssssss
s ssssssssss

DFKEDGNILG HKLEYNYNSH NVYIMADKQK NGIKVNFKIR HNIEDGSVQL

dfkedgnilg hkleynynsh nvyimadkqk ngikvnfkir hniedgsvql
hhh

179
1179

ssshhh

idykfgltkv ffrpgkfaef dqimksdpdh laelvkrvnh wlicsrwkkv

h
hh

129
1129

hhhhh

hhhhh hhhhh

ssssshhhhh hhh

sssssssss
sssssssss

TARGET
4anjA

TARGET
4anjA

sssss sss

hhhhhhhhhh hhhhhhhhhh

TARGET
4anjA

TARGET
4anjA

hhhhhhhh

vldlmqggfp srasfhelyn mykkympdkl arldprlfck alfkalglne

sssss sss sss

TARGET
4anjA

TARGET
4anjA

hhhhsss

fktqlnllld klrstgasfi rcikpnlkmt shhfegaqil sqlqcsgmvs

hhhhh

4anjA

TARGET
4anjA

sssssss

hhhhhhhhhh hhh

4anjA

4anjA

hfagavcyet tqfveknnda lhmsleslic esrdkfirel fesfisvgnk

sss
sss

s sssssss
s sssssss

sssssssss ssss
sssssssss ssss

ssss
ssss

ADHYQQNTPI GDGPVLLPDN HYLSTQSALS KDPNEKRDHM VLLEFVTAAG

adhyqqntpi gdgpvllpdn hylsyqsals kdpnekrdhm vllefvtaag
ssssssssss
ssssssssss

ssssssssss
ssssssssss

sss sssssssss
sss sssssssss

TARGET
4anjA

TARGET
4anjA

Modeling Log:
3.70 (SP3)
Loading Template: 4anjA.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
Building CSP loop with anchor residues PHE 64 and VAL 68
Number of Ligations found: 68
ACCEPTING loop
31: clash=
0 FF=
1186.0 PP= -2.00
Optimizing Sidechains
Adding Hydrogens
Optimizing loops and OXT (nb = 5)
Final Total Energy:
-11155.463 KJ/mol
Dumping Sequence Alignment

Template Selection Log:

- Start SMR-Pipeline in automated mode on BC2-cluster at Wed Oct 23 18:23:39 2013

- User specified template structure by a PDB identifier(4anjA), entering user template mode

- Aligning sequence of the user template structure with the target sequence using BLAST
- Blast template search was successfull, number of templates selected for modeling: 1; entering modeling mo
- Send 1 target-template alignments for modeling
-

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
*****************************************************************************
building model based on 4anjA (1-228) was successfull
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
residues to model an additional template :

50
25

- Finish SMR-Pipeline in automated mode on BC2-cluster at Wed Oct 23 18:26:56 2013

Quaternary Structure Annotation of the Template

4anj is annotated as HETERO DIMER
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: 4anj.pdb1.gz
Quaternary Structure Modelling of the Target Protein
4anj_1 is labeled HETERO oligomeric, i.e the sequences of the chains are not identical
Modeling of hetero oligomers is not yet supported by the SWISS-MODEL automated modeling pipeline
Please use the advancend features of the SwissModel Project Mode
The final model was calculated as single chain
Ligand Modeling Log: Templates ligands section
Ligands in the template: ADP: 1, ALA: 1, ALF: 1, MG: 1.
Ligands in the template that will be assessed: ADP2230, MG2231.
Models ligands section
ADP2230
ADP2230 interacts, within a radius of 3 Angstroem, with the following ions: MG2231. They will be considered as a single
ligand.
There are not residues in the model that match the ones that interact with the ligand in the template.
Given the properties calculated previously, the ligand A.ADP2230 will not be included in the model.
ADP2230: 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.