SWISS-MODEL Repository - Model Details

Model Overview
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1
536

Sequence
UniProt Q01064 Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (63 kDa Cam-PDE)
Homo sapiens (Human).
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

STRING
Q01064: 9606.ENSP0000024

Domain
Link to: [ InterPro ]
PDEase_I
PDEase_I_N

Model 3D Structure
Model information:
Modelled residue range: 146 to 502
Based on template: [ 1taz ]  
Sequence Identity [%]: 89%
Model date: 2014-07-17
Revision date: 2014-07-15

Quaternary structure information: [details]
Template (1taz): MONOMER
Model: MONOMER

Ligand information: [details]
Ligands in the template: 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       VGPTYSTA VLNCLKNLDL WCFDVFSLNQ AADDHALRTI VFELLTRHNL
1taz_1#1  146     vgptysta vlnclknldl wcfdvfslnq aaddhalrti vfelltrhnl
                                                                      
TARGET                  hh hhhhh          hhhhhh h    hhhhh hhhhhh   h
1taz_1#1                hh hhhhh          hhhhhh hh   hhhhh hhhhhh   h


TARGET    49    ISRFKIPTVF LMSFLDALET GYGKYKNPYH NQIHAADVTQ TVHCFLLRTG
1taz_1#1  194   isrfkiptvf lmsfldalet gygkyknpyh nqihaadvtq tvh-fllrtg
                                                                      
TARGET          hhhh   hhh hhhhhhhhhh h           hhhhhhhhh hhhhhhhh  
1taz_1#1        hhhh   hhh hhhhhhhhhh h           hhhhhhhhh h    hhh  


TARGET    99    MVHCLSEIEL LAIIFAAAIH DYEHTGTTNS FHIQTKSECA IVYNDRSVLE
1taz_1#1  244   mvhclseiel laiifaaaih dyehtgttns fhiqtkseca ivyndrsvle
                                                                      
TARGET           hh   hhhh hhhhhhhhh          hh hhh   hhhh hhh    hhh
1taz_1#1         hh   hhhh hhhhhhhhh          hh hhh   hhhh hhh    hhh


TARGET    149   NHHISSVFRL MQDDEMNIFI NLTKDEFVEL RALVIEMVLA TDMSCHFQQV
1taz_1#1  294   nhhissvfrl mqddemnifi nltkdefvel ralviemvla tdmschfqqv
                                                                      
TARGET          hhhhhhhhhh h             hhhhhhh hhhhhhhhhh       hhhh
1taz_1#1        hhhhhhhhhh h             hhhhhhh hhhhhhhhhh       hhhh


TARGET    199   KTMKTALQQL ERIDKPKALS LLLHAADISH PTKQWLVHSR WTKALMEEFF
1taz_1#1  344   ktmktalqq- -ridkpkals lllhaadish ptkqwlvhsr wtkalmeeff
                                                                      
TARGET          hhhhhhhh       hhhhhh hhhhhh   h h   hhhhhh hhhhhhhhhh
1taz_1#1        hhhhhhhh       hhhhhh hhhhhh   h h   hhhhhh hhhhhhhhhh


TARGET    249   RQGDKEAELG LPFSPLCDRT STLVAQSQIG FIDFIVEPTF SVLTDVAEKS
1taz_1#1  394   rqgdkeaelg lp------rt stlvaqsqig fidfiveptf svltdvaeks
                                                                      
TARGET          hhhhhhhhh             hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh
1taz_1#1        hhhhhhhhh              hhhhhhhhh hhhhhhhhhh hhhhhhhhhh


TARGET    299   VQPLADEDSK SKNQPSFQWR QPSLDVEVGD PNPDVVSFRS TWVKRIQENK
1taz_1#1  444   vq-------- ---------- ---------d pnpdvvsfrs twvkriqenk
                                                                      
TARGET          h              hhhhhh hhhhhhhh     hhhhhhhh hhhhhhhhhh
1taz_1#1                                           hhhhhhhh hhhhhhhhhh


TARGET    349   QKWKERAAS                                             
1taz_1#1  494   qkwkeraas-                                            
                                                                      
TARGET          hhhhhhhh                                              
1taz_1#1        hhhhhhhh                                              



Quality


Template's ligands section
Ligands in the template: MG: 1, ZN: 1.
Ligands in the template that will be assessed: MG2, ZN1.
Model's ligands section
ZN1
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: 0.040
Given the properties calculated previously, the ligand z.ZN1 will be included in the final model.
ZN1: conservation:True, RMSD:True, included: True

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

The new model with the included ligands was saved successfully.


Quaternary Structure Annotation of the Template
1taz 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: 1taz.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 0.616 (>0.5 indicates similarity)
Model was succesfully built as MONOMER.


Template Selection
 - Start SMR-Pipeline for:5b8da34458173e3f3cd5c0b538008767 on BC2-cluster at Thu Jul 17 02:52:12
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...
FATAL - No templates found in HHSEARCH, strange - make sure all DBs are sync'ed correctly
 - 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 1tazA (146-502) 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 Thu Jul 17 02:55:31
2014 




Template Description
Match Chain SeqId

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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