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Model Overview
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1
640

Sequence
UniProt Q8BH04
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
PEPCK

Model 3D Structure
Model information:
Modelled residue range: 32 to 640
Based on template: [ 3dtb ]  
Sequence Identity [%]: 72%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3dtb): DIMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: 1PE: 1, BCT: 1, EPE: 1, GDP: 1, MN: 2, NA: 1, PGA: 1.
Ligands in the model: GDP: 1, MN: 2
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                    VLSGDM SQLPAGVRDF VARSAHLCQP EGIHICDGTE
3dtbA     3     pqlhngldfs ak--viqgsl dslpqevrkf vegnaqlcqp eyihicdgse
                                                                      
TARGET                                    hhhhhh hhhhhhhh    sssss   h
3dtbA                    h h              hhhhhh hhhhhhhh    sssss   h


TARGET    37    AENTAILALL EEQGLIRKLP KYKNCWLART DPKDVARVES KTVIVTPSQR
3dtbA     51    eeygrllahm qeegvirklk kydncwlalt dprdvaries ktviitqeqr
                                                                      
TARGET          hhhhhhhhhh hhh   sss      ssss              sssss    h
3dtbA           hhhhhhhhhh hhh   sss      ssss              sssss    h


TARGET    87    DTVPLLAGGA RGQLGNWMSP DEFQRAVDER FPGCMQGRIM YVLPFSMGPV
3dtbA     101   dtvpipksg- qsqlgrwmse edfekafnar fpgcmkgrtm yvipfsmgpl
                                                                      
TARGET          hh                  h hhhhhhhh            s sssssss   
3dtbA           hh                  h hhhhhhhh            s sssssss   


TARGET    137   GSPLSRIGVQ LTDSAYVVAS MRIMTRLGTP VLQALGDGDF IKCLHSVGQP
3dtbA     150   gsplakigie ltdspyvvas mrimtrmgts vlealgdgef ikclhsvgcp
                                                                      
TARGET               sssss ss  hhhhhh hhhh sss h hhhhh      ssssss    
3dtbA                sssss ss  hhhhhh hhhh sss h hhhhh      ssssss    


TARGET    187   LTGHGDPVGQ WPCNPEKTLI GHVPDQREIV SFGSGYGGNS LLGKKCFALR
3dtbA     200   lplkkplvnn wacnpeltli ahlpdrreii sfgsgyggns llgkkcfalr
                                                                      
TARGET                             ss ssss  ssss sss            hhhhhh
3dtbA                              ss ssss  ssss sss            hhhhhh


TARGET    237   IASRLARDEG WLAEHMLILG ITNPAGKKRY VAAAFPSACG KTNLAMMRPA
3dtbA     250   iasrlakeeg wlaehmlilg itnpegkkky laaafpsacg ktnlammnpt
                                                                      
TARGET          hhhhhhhhh   sssssssss ssss  ssss ssss       hhhhh     
3dtbA           hhhhhhhh    sssssssss ssss  ssss ssss       hhhhh     


TARGET    287   LPGWKVECVG DDIAWMRFDS EGQLRAINPE NGFFGVAPGT SAATNPNAMA
3dtbA     300   lpgwkvecvg ddiawmkfda qgnlrainpe ngffgvapgt svktnpnaik
                                                                      
TARGET            ssssssss sssssssss    sssss    sssssss         hhhhh
3dtbA             ssssssss sssssssss    sssss    sssssss         hhhhh


TARGET    337   TIQSNTLFTN VAETSDGGVY WEGIDQPLPP GVTITSWLGK PWKPGDKEPC
3dtbA     350   tiqkntiftn vaetsdggvy wegideplap gvtitswknk ewrpqdeepc
                                                                      
TARGET          hh   sssss  ssss  sss              ssss   s ss        
3dtbA           hh   sssss  ssss  sss              ssss   s ss        


TARGET    387   AHPNSRFCVP ARQCPIMDPA WEAPEGVPID AIIFGGRRPK GVPLVYEAFN
3dtbA     400   ahpnsrfctp asqcpiidpa wespegvpie giifggrrpa gvplvyeals
                                                                      
TARGET              ssssss s                ssss ssss          sssss  
3dtbA               ssssss s                ssss sssss         sssss  


TARGET    437   WRHGVFVGSA MRSESTAAAE HKGKTIMHDP FAMRPFFGYN FGRYLEHWLS
3dtbA     450   wqhgvfvgaa mrseataaae hkgkvimhdp famrpffgyn fgkylahwls
                                                                      
TARGET          hhhhhhhhhh sssss          sssss             hhhhhhhhhh
3dtbA           hhhhhhhhh  sssss          sssss             hhhhhhhhhh


TARGET    487   MEGQKGARLP RIFHVNWFRR DEAGRFLWPG FGENARVLDW ICRRLEGEDS
3dtbA     500   mahrpaaklp kifhvnwfrk dkngkflwpg fgensrvlew mfgriegeds
                                                                      
TARGET          hh         ssssss  ss s   sss      hhhhhhhh hhhhhh   s
3dtbA           hh         ssssss  ss s   sss      hhhhhhhh hhhhhh   s


TARGET    537   AQETPIGLVP KEGALDLSGL SAVDTSQLFS IPKDFWEQEV RDIRGYLTEQ
3dtbA     550   akltpigyvp kedalnlkgl gdvnveelfg iskefwekev eeidkyledq
                                                                      
TARGET          ssss  ssss s              hhhhh    hhhhhhhh hhhhhhhhhh
3dtbA           ssss  ssss s              hhhhh    hhhhhhhh hhhhhhhhhh


TARGET    587   VNQDLPKEVL AELEALEGRV QKM                             
3dtbA     600   vnadlpyeie relralkqri sqm-                            
                                                                      
TARGET                hhhh hhhhhhhhhh h                               
3dtbA                 hhhh hhhhhhhhhh h                               



Quality


Template's ligands section
Ligands in the template: 1PE: 1, BCT: 1, EPE: 1, GDP: 1, MN: 2, NA: 1, PGA: 1.
Ligands in the template that will be assessed: GDP800, MN700, MN701, NA1100.
Model's ligands section
GDP800
GDP800 interacts, within a radius of 3 Angstroem, with the following ions: MN701. They will be considered as a single ligand.
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: 0.080
Given the properties calculated previously, the ligand A.GDP800 will be included in the model.
GDP800: conservation:True, RMSD:True, included: True

MN700
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: 0.070
Given the properties calculated previously, the ligand A.MN700 will be included in the final model.
MN700: conservation:True, RMSD:True, included: True

NA1100
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand A.NA1100 will not be included in the final model.
NA1100: conservation:False, RMSD:False, included: False

The new model with the included ligands was saved successfully.


Quaternary Structure Annotation of the Template
3dtb is annotated as 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: 3dtb.pdb3.gz

Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=DIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.098 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 3dtbB


Template Selection
 - Start SMR-Pipeline for:5c0fdd6441f87bb4919fe3cb3b2e9627 on BC2-cluster at Fri Feb 22 19:21:48
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 3dtbA (32-640) 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:5c0fdd6441f87bb4919fe3cb3b2e9627 on BC2-cluster at Fri Feb 22 19:24:43
2013 




Template Description
Match Chain SeqId

3dt4: THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH OXALATE AND GTP
Solved by: X-RAY, Resolution: 1.45A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 3dt4A 73%
[Model]
32-640 3dt4C 73%
[Model]

3dt2: THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH OXALATE AND GTP
Solved by: X-RAY, Resolution: 1.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 3dt2A 73%
[Model]

3moe: THE STRUCTURE OF RAT CYTOSOLIC PEPCK MUTANT A467G IN COMPLBETA-SULFOPYRUVATE AND GTP
Solved by: X-RAY, Resolution: 1.25A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 3moeA 72%
[Model]

3moh: THE STRUCTURE OF RAT CYTOSOLIC PEPCK MUTANT A467G IN COMPLPHOSPHOGLYCOLATE AND GDP
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 3mohA 71%
[Model]
32-640 3mohB 71%
[Model]

2qf2: RAT CYTOSOLIC PEPCK IN COMPLEX WITH OXALOACETIC ACID AND GDP.
Solved by: X-RAY, Resolution: 1.65A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2qf2A 73%
[Model]
32-640 2qf2B 71%
[Model]

2qew: RAT CYTOSOLIC PEPCK, IN COMPLEX WITH MANGANESE ION.
Solved by: X-RAY, Resolution: 1.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2qewA 71%
[Model]

2rkd: THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH 3- PHOSPHONOPROPIONATE
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2rkdA 71%
[Model]

3mof: THE STRUCTURE OF RAT CYTOSOLIC PEPCK MUTANT A467G IN COMPLOXALATE AND GTP
Solved by: X-RAY, Resolution: 1.75A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 3mofA 72%
[Model]
32-640 3mofB 71%
[Model]

2rka: THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH PHOSPHOGLYCOLATE
Solved by: X-RAY, Resolution: 1.95A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2rkaA 71%
[Model]
32-640 2rkaC 72%
[Model]

3dtb: THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH PHOSPHOGLYCOLATE AND GDP
Solved by: X-RAY, Resolution: 1.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 3dtbB 71%
[Model]
32-640 3dtbA 73%
[Model]

2rk8: THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH PHOSPHONOFORMATE
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2rk8A 73%
[Model]
32-640 2rk8B 71%
[Model]

3dt7: THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH BETA-SULFOPYRUVATE AND GTP
Solved by: X-RAY, Resolution: 1.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 3dt7A 73%
[Model]
32-640 3dt7B 71%
[Model]

2qf1: RAT CYTOSOLIC PEPCK IN COMPLEX WITH OXALOACETIC ACID.
Solved by: X-RAY, Resolution: 1.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2qf1A 71%
[Model]

2rk7: THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH OXALA
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2rk7A 71%
[Model]
32-640 2rk7B 72%
[Model]

2rke: THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH SULFOACETATE.
Solved by: X-RAY, Resolution: 1.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2rkeA 71%
[Model]

2qey: RAT CYTOSOLIC PEPCK IN COMPLEX WITH GTP
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2qeyA 71%
[Model]

2gmv: PEPCK COMPLEX WITH A GTP-COMPETITIVE INHIBITOR
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 2gmvA 69%
[Model]
32-640 2gmvB 69%
[Model]

1khf: PEPCK COMPLEX WITH PEP
Solved by: X-RAY, Resolution: 2.02A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 1khfA 69%
[Model]

1khg: PEPCK
Solved by: X-RAY, Resolution: 2.34A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 1khgA 69%
[Model]

1nhx: PEPCK COMPLEX WITH A GTP-COMPETITIVE INHIBITOR
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 1nhxA 69%
[Model]

1m51: PEPCK COMPLEX WITH A GTP-COMPETITIVE INHIBITOR
Solved by: X-RAY, Resolution: 2.25A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 1m51A 69%
[Model]

2fah: THE STRUCTURE OF MITOCHONDRIAL PEPCK, COMPLEX WITH MN AND GDP
Solved by: X-RAY, Resolution: 2.09A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

33-640 2fahA 69%
[Model]
33-640 2fahB 69%
[Model]
33-640 2fahC 69%
[Model]
33-640 2fahD 69%
[Model]

1khb: PEPCK COMPLEX WITH NONHYDROLYZABLE GTP ANALOG, NATIVE DATA
Solved by: X-RAY, Resolution: 1.85A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 1khbA 69%
[Model]

1khe: PEPCK COMPLEX WITH NONHYDROLYZABLE GTP ANALOG, MAD DATA
Solved by: X-RAY, Resolution: 2.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-640 1kheA 69%
[Model]

2faf: THE STRUCTURE OF CHICKEN MITOCHONDRIAL PEPCK.
Solved by: X-RAY, Resolution: 1.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

33-640 2fafA 68%
[Model]
33-640 2fafB 68%
[Model]

2qzy: THE STRUCTURE OF CHICKEN MITOCHONDRIAL PEPCK IN COMPLEX WITH PEP
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

33-640 2qzyA 68%
[Model]
33-640 2qzyB 68%
[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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