SWISS-MODEL Repository - Model Details

Model Overview
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1
536

Sequence
UniProt Q01064
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q01064: 9606.ENSP0000024

Domain
Link to: [ InterPro ]
PDEase_I
PDEase_I_N

Model 3D Structure
Model information:
Modelled residue range: 151 to 502
Based on template: [ 4npv ]  
Sequence Identity [%]: 91%
Model date: 2014-09-19
Revision date: 2014-09-17

Quaternary structure information: [details]
Template (4npv): MONOMER
Model: MONOMER

Ligand information: [details]
Ligands in the template: 0NK: 1, MG: 1, ZN: 1.
Ligands in the model: ZN: 1
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment

TARGET    1       STAVLNCL KNLDLWCFDV FSLNQAADDH ALRTIVFELL TRHNLISRFK
4npv_1#1  151     stavlncl knldlwcfdv fslnqaaddh alrtivfell trhnlisrfk
                                                                      
TARGET             hhhhhhh          h hhhhhhh    hhhhhhhhhh h   hhhhh 
4npv_1#1           hhhhhhh          h hhhhhhh    hhhhhhhhhh h   hhhhh 


TARGET    49    IPTVFLMSFL DALETGYGKY KNPYHNQIHA ADVTQTVHCF LLRTGMVHCL
4npv_1#1  199   iptvflmsfl daletgygky knpyhnqiha advtqtvhcf llrtgmvhcl
                                                                      
TARGET            hhhhhhhh hhhhhhhhh         hhh hhhhhhhhhh hhhh      
4npv_1#1          hhhhhhhh hhhhhhhhh         hhh hhhhhhhhhh hhh   hh  


TARGET    99    SEIELLAIIF AAAIHDYEHT GTTNSFHIQT KSECAIVYND RSVLENHHIS
4npv_1#1  249   seiellaiif aaaihdyeht gttnsfhiqt ksecaivynd rsvlenhhis
                                                                      
TARGET           hhhhhhhhh hhhh          hhhhh    hhhhhhh     hhhhhhhh
4npv_1#1         hhhhhhhhh hhhh          hhhhh    hhhhhhh     hhhhhhhh


TARGET    149   SVFRLMQDDE MNIFINLTKD EFVELRALVI EMVLATDMSC HFQQVKTMKT
4npv_1#1  299   svfrlmqdde mnifinltkd efvelralvi emvlatdmsc hfqqvktmkt
                                                                      
TARGET          hhhhhh             hh hhhhhhhhhh hhhhh       hhhhhhhhh
4npv_1#1        hhhhhh        hh   hh hhhhhhhhhh hhhhh   hh hhhhhhhhhh


TARGET    199   ALQQLERIDK PKALSLLLHA ADISHPTKQW LVHSRWTKAL MEEFFRQGDK
4npv_1#1  349   alqqleridk pkalslllha adishptkqw lvhsrwtkal meeffrqgdk
                                                                      
TARGET          hhh      h hhhhhhhhhh h   hh   h hhhhhhhhhh hhhhhhhhhh
4npv_1#1        hhh      h hhhhhhhhhh h   hh   h hhhhhhhhhh hhhhhhhhhh


TARGET    249   EAELGLPFSP LCDRTSTLVA QSQIGFIDFI VEPTFSVLTD VAEKSVQPLA
4npv_1#1  399   eaelglpfsp lcdrtstlva qsqigfidfi veptfsvltd vaeksvqp--
                                                                      
TARGET          hhhh                h hhhhhhhhhh hhhhhhhhhh hhhh    hh
4npv_1#1        hhhh                h hhhhhhhhhh hhhhhhhhhh hhhh      


TARGET    299   DEDSKSKNQP SFQWRQPSLD VEVGDPNPDV VSFRSTWVKR IQENKQKWKE
4npv_1#1  476   ---------- ---------- -------pdv vsfrstwvkr iqenkqkwke
                                                                      
TARGET          hhhhhhhhhh hhhhh               h hhhhhhhhhh hhhhhhhhhh
4npv_1#1                                       h hhhhhhhhhh hhhhhhhhhh


TARGET    349   RAAS                                                  
4npv_1#1  499   raas-                                                 
                                                                      
TARGET          hh                                                    
4npv_1#1        hh                                                    



Quality


Template's ligands section
Ligands in the template: 0NK: 1, MG: 1, ZN: 1.
Ligands in the template that will be assessed: MG2, ZN3.
Model's ligands section
MG2
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand z.MG2 will not be included in the final model.
MG2: conservation:False, RMSD:False, included: False

ZN3
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 smaller than 2 Angstrom: 0.030
Given the properties calculated previously, the ligand z.ZN3 will be included in the final model.
ZN3: conservation:True, RMSD:True, included: True

The new model with the included ligands was saved successfully.


Quaternary Structure Annotation of the Template
4npv is annotated as MONOMER
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: 4npv.pdb1.gz

Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template can be assumed to be similar (=MONOMER)
The corresponding reliability score is 0.614 (>0.5 indicates similarity)
Model was succesfully built as MONOMER.


Template Selection
 - Start SMR-Pipeline for:5b8da34458173e3f3cd5c0b538008767 on BC2-cluster at Fri Sep 19 19:38:01
2014 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - Skip Template HHsearch issue
 - Skip Template HHsearch issue
 - Skip Template HHsearch issue
 - No template with C found
 - No template with D found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                        *****************************************************
 - building model based on 4npvA (151-502) was successful 
 - Repository 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 :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:5b8da34458173e3f3cd5c0b538008767 on BC2-cluster at Fri Sep 19 19:41:36
2014 




Template Description
Match Chain SeqId

4npv: CRYSTAL STRUCTURE OF HUMAN PDE1B BOUND TO INHIBITOR 7A (6,TRIMETHOXY-N-(PENTAN-3-YL)QUINAZOLIN-4-AMINE)
Solved by: X-RAY, Resolution: 2.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

151-502 4npvA 92%
[Model]

4npw: CRYSTAL STRUCTURE OF HUMAN PDE1B BOUND TO INHIBITOR 19A (7DIMETHOXY-N-[(2S)-1-(3-METHYL-1H-PYRAZOL-5-YL)PROPAN-2-YL4-AMINE)
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

150-502 4npwA 91%
[Model]

1taz: CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 1B
Solved by: X-RAY, Resolution: 1.77A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

146-502 1tazA 90%
[Model]

Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.




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