SWISS-MODEL Repository - Model Details

Model Overview
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1
277

Sequence
UniProt P52623
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
PRK

Model 3D Structure
Model information:
Modelled residue range: 22 to 235
Based on template: [ 2jeo ]  
Sequence Identity [%]: 94%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2jeo): TETRAMER
Model: TETRAMER

Ligand information: [details]
Ligands in the template: none.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2013-01-30. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment 

TARGET    1        RPFLIGV SGGTASGKST VCEKIMELLG QNEVDRRQRK LVILSQDCFY
2jeo_1#2  21    m--rpfligv sggtasgkst vcekimellg qneveqrqrk vvilsqdrfy
                                                                      
TARGET               sssss s      hhh hhhhhhhhh           s ssssss  ss
2jeo_1#2             sssss s      hhh hhhhhhhhh           s sssssshhss


TARGET    48    KVLTAEQKAK ALKGQYNFDH PDAFDNDLMH KTLKNIVEGK TVEVPTYDFV
2jeo_1#2  69    kvltaeqkak alkgqynfdh pdafdndlmh rtlknivegk tvevptydfv
                                                                      
TARGET          s   hhhhhh h            ssshhhhh hhhhhhhh    sss sss  
2jeo_1#2        s   hhhhhh h            ssshhhhh hhhhhhhh    sss sss  


TARGET    98    THSRLPETTV VYPADVVLFE GILVFYTQEI RDMFHLRLFV DTDSDVRLSR
2jeo_1#2  119   thsrlpettv vypadvvlfe gilvfysqei rdmfhlrlfv dtdsdvrlsr
                                                                      
TARGET            sss   ss s   ssssss s      hhh hh   sssss s  hhhhhhh
2jeo_1#2          sss   ss s   ssssss s      hhh hh   sssss s  hhhhhhh


TARGET    148   RVLRDVQRGR DLEQILTQYT AFVKPAFEEF CLPTKKYADV IIPRGVDNMV
2jeo_1#2  169   rvlrdv---r dleqiltqyt tfvkpafeef clptkkyadv iiprgvdnmv
                                                                      
TARGET          hhh   hh     hhhhhhhh hhhhhhhhhh hh   h   s ssss    hh
2jeo_1#2        hhhhh       hhhhhhhhh hhhhhhhhhh hh   h   s ssss    hh


TARGET    198   AINLIVQHIQ DILNGDL --  RPFLIGVSG GTASGKSTVC EKIMELLGQN
2jeo_1#2  219   ainlivqhiq dilngdi-m- -rpfligvsg gtasgkstvc ekimellgqn
                                    *                                 
TARGET          hhhhhhhhhh hhhh          ssssss       hhhhh hhhhhhh   
2jeo_1#2        hhhhhhhhhh hhhh          ssssss       hhhhh hhhhhhh   


TARGET    244   EVDRRQRKLV ILSQDCFYKV LTAEQKAKAL KGQYNFDHPD AFDNDLMHKT
2jeo_1#2  51    eveqrqrkvv ilsqdrfykv ltaeqkakal kgqynfdhpd afdndlmhrt
                                                                      
TARGET                 sss ssss  sss    hhhhhhh             ssshhhhhhh
2jeo_1#2               sss sssshhsss    hhhhhhh             ssshhhhhhh


TARGET    294   LKNIVEGKTV EVPTYDFVTH SRLPETTVVY PADVVLFEGI LVFYTQEIRD
2jeo_1#2  101   lknivegktv evptydfvth srlpettvvy padvvlfegi lvfysqeird
                                                                      
TARGET          hhhhhh   s ss sss     sss   sss    sssssss       hhhhh
2jeo_1#2        hhhhhh   s ss sss     sss   sss    sssssss       hhhhh


TARGET    344   MFHLRLFVDT DSDVRLSRRV LRDVQRGRDL EQILTQYTAF VKPAFEEFCL
2jeo_1#2  151   mfhlrlfvdt dsdvrlsrrv lrdv---rdl eqiltqyttf vkpafeefcl
                                                                      
TARGET             ssssss   hhhhhhhhh h   hh     hhhhhhhh    hhhhhhhhh
2jeo_1#2           ssssss   hhhhhhhhh hhh      h hhhhhhhhhh hhhhhhhhhh


TARGET    394   PTKKYADVII PRGVDNMVAI NLIVQHIQDI LNGDL -- R PFLIGVSGGT
2jeo_1#2  201   ptkkyadvii prgvdnmvai nlivqhiqdi lngdi-m--r pfligvsggt
                                                        *             
TARGET             h   sss ss    hhhh hhhhhhhhhh hh          ssssss   
2jeo_1#2           h   sss ss    hhhh hhhhhhhhhh hh          ssssss   


TARGET    440   ASGKSTVCEK IMELLGQNEV DRRQRKLVIL SQDCFYKVLT AEQKAKALKG
2jeo_1#2  33    asgkstvcek imellgqnev eqrqrkvvil sqdrfykvlt aeqkakalkg
                                                                      
TARGET             hhhhhhh hhhhh           sssss ss  sss    hhhhhhh   
2jeo_1#2           hhhhhhh hhhhh           sssss sshhsss    hhhhhhh   


TARGET    490   QYNFDHPDAF DNDLMHKTLK NIVEGKTVEV PTYDFVTHSR LPETTVVYPA
2jeo_1#2  83    qynfdhpdaf dndlmhrtlk nivegktvev ptydfvthsr lpettvvypa
                                                                      
TARGET                  ss shhhhhhhhh hhhh   sss  sss    ss s   sss   
2jeo_1#2                ss shhhhhhhhh hhhh   sss  sss    ss s   sss   


TARGET    540   DVVLFEGILV FYTQEIRDMF HLRLFVDTDS DVRLSRRVLR DVQRGRDLEQ
2jeo_1#2  133   dvvlfegilv fysqeirdmf hlrlfvdtds dvrlsrrvlr dv---rdleq
                                                                      
TARGET          sssssss       hhhhh    ssssss  h hhhhhhhhh    hh    hh
2jeo_1#2        sssssss       hhhhh    ssssss  h hhhhhhhhhh h      hhh


TARGET    590   ILTQYTAFVK PAFEEFCLPT KKYADVIIPR GVDNMVAINL IVQHIQDILN
2jeo_1#2  183   iltqyttfvk pafeefclpt kkyadviipr gvdnmvainl ivqhiqdiln
                                                                      
TARGET          hhhhhhhhhh hhhhhhhh    h   sssss     hhhhhh hhhhhhhhhh
2jeo_1#2        hhhhhhhhhh hhhhhhhh    h   sssss     hhhhhh hhhhhhhhhh


TARGET    640   GDL -- RPF LIGVSGGTAS GKSTVCEKIM ELLGQNEVDR RQRKLVILSQ
2jeo_1#2  233   gdi-m--rpf ligvsggtas gkstvcekim ellgqneveq rqrkvvilsq
                     *                                                
TARGET                   s sssss       hhhhhhhhh hhh           sssssss
2jeo_1#2                 s sssss       hhhhhhhhh hhh           sssssss


TARGET    686   DCFYKVLTAE QKAKALKGQY NFDHPDAFDN DLMHKTLKNI VEGKTVEVPT
2jeo_1#2  65    drfykvltae qkakalkgqy nfdhpdafdn dlmhrtlkni vegktvevpt
                                                                      
TARGET            sss   hh hhhhh            sssh hhhhhhhhhh hh   sss s
2jeo_1#2        hhsss   hh hhhhh            sssh hhhhhhhhhh hh   sss s


TARGET    736   YDFVTHSRLP ETTVVYPADV VLFEGILVFY TQEIRDMFHL RLFVDTDSDV
2jeo_1#2  115   ydfvthsrlp ettvvypadv vlfegilvfy sqeirdmfhl rlfvdtdsdv
                                                                      
TARGET          ss    sss    sss   ss sssss       hhhhh   s sssss  hhh
2jeo_1#2        ss    sss    sss   ss sssss       hhhhh   s sssss  hhh


TARGET    786   RLSRRVLRDV QRGRDLEQIL TQYTAFVKPA FEEFCLPTKK YADVIIPRGV
2jeo_1#2  165   rlsrrvlrdv ---rdleqil tqyttfvkpa feefclptkk yadviiprgv
                                                                      
TARGET          hhhhhhh    hh    hhhh hhhh   hhh hhhhhh   h    sssss  
2jeo_1#2        hhhhhhhhh       hhhhh hhhhhhhhhh hhhhhh   h    sssss  


TARGET    836   DNMVAINLIV QHIQDILNGD L                               
2jeo_1#2  215   dnmvainliv qhiqdilngd i-                              
                                                                      
TARGET            hhhhhhhh hhhhhhhh                                   
2jeo_1#2          hhhhhhhh hhhhhhhh

Quality 


Template's ligands section 
Template without ligands. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 2jeo 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: 2jeo.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 (=TETRAMER) 
 The corresponding reliability score is 0.89 (>0.5 indicates similarity) 
 Model was succesfully built as TETRAMER.

Template Selection 
 - Start SMR-Pipeline for:0679a83ac677847106f498501ab954e6 on BC2-cluster at Sat Feb 23 04:25:46
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

FATAL - No A3m 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 2jeoA (22-235) 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:0679a83ac677847106f498501ab954e6 on BC2-cluster at Sat Feb 23 04:31:37
2013


Template Description
Match Chain SeqId

2uvq: CRYSTAL STRUCTURE OF HUMAN URIDINE-CYTIDINE KINASE 1 IN COMPLEX WITH ADP
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

22-235 2uvqA 95%
[Model]

2jeo: CRYSTAL STRUCTURE OF HUMAN URIDINE-CYTIDINE KINASE 1
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

22-235 2jeoA 95%
[Model]

1uj2: CRYSTAL STRUCTURE OF HUMAN URIDINE-CYTIDINE KINASE 2 COMPLEXED WITH PRODUCTS, CMP AND ADP
Solved by: X-RAY, Resolution: 1.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

23-233 1uj2B 80%
[Model]
23-233 1uj2A 80%
[Model]

1xrj: RAPID STRUCTURE DETERMINATION OF HUMAN URIDINE-CYTIDINE KINASE 2 USING A CONVENTIONAL LABORATORY X-RAY SOURCE ANDA SINGLE SAMARIUM DERIVATIVE
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

23-233 1xrjB 80%
[Model]
23-232 1xrjA 80%
[Model]

1ufq: CRYSTAL STRUCTURE OF LIGAND-FREE HUMAN URIDINE-CYTIDINE KINASE 2
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

23-232 1ufqC 80%
[Model]
23-232 1ufqA 80%
[Model]
23-232 1ufqD 80%
[Model]
23-232 1ufqB 79%
[Model]

1uej: CRYSTAL STRUCTURE OF HUMAN URIDINE-CYTIDINE KINASE 2 COMPLEXED WITH A SUBSTRATE, CYTIDINE
Solved by: X-RAY, Resolution: 2.61A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

23-231 1uejA 78%
[Model]
23-232 1uejB 78%
[Model]

1uei: CRYSTAL STRUCTURE OF HUMAN URIDINE-CYTIDINE KINASE 2 COMPLEXED WITH A FEEDBACK-INHIBITOR, UTP
Solved by: X-RAY, Resolution: 2.60A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

23-232 1ueiA 77%
[Model]
23-233 1ueiB 78%
[Model]

1udw: CRYSTAL STRUCTURE OF HUMAN URIDINE-CYTIDINE KINASE 2 COMPLEXED WITH A FEEDBACK-INHIBITOR, CTP
Solved by: X-RAY, Resolution: 2.60A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

23-232 1udwA 77%
[Model]
23-233 1udwB 78%
[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.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.