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Model Overview
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1
332

Sequence
UniProt Q95028
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q95028: 7227.FBpp0076716

Domain
Link to: [ InterPro ]
Ldh_1_N
Ldh_1_C

Model 3D Structure
Model information:
Modelled residue range: 3 to 332
Based on template: [ 4aj2 ]  
Sequence Identity [%]: 61%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (4aj2): TETRAMER
Model: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: 52C: 1, MLI: 3.
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       AIKDSLLA Q-VAEVLPSS GHKVTIVGIG QVGMASAFSI LAQNVSKEVC
4aj2D     2       alkdqliv nllkeevpqn --kitvvgvg avgmacaisi lmkdladela
                                                                      
TARGET             hhhhh                 sssss   hhhhhhhhhh hhh    sss
4aj2D              hhhhh                 sssss   hhhhhhhhhh hhh    sss


TARGET    48    LIDVCADKLQ GELMDLQHGS NFLKNPQITA STDFAASANS RLCIVTAGVR
4aj2D     49    lvdviedklk gemmdlqhgs lflktpkivs skdysvtans klviitagar
                                                                      
TARGET          ss   hhhhh hhhhhhh          ssss s   hh     ssssss    
4aj2D           ss   hhhhh hhhhhhh    h     ssss s   hh     ssssss    


TARGET    98    QKEGESRLSL VQRNTDILKN IIPKLVEYSP DTILLMVSNP VDIMTYVAWK
4aj2D     99    qqegesrlnl vqrnvnifkf iipnvvkysp qckllivsnp vdiltyvawk
                                                                      
TARGET                 h    hhhhhhhhh hhhhhhhh     sssss    hhhhhhhhhh
4aj2D                  h    hhhhhhhhh hhhhhhhh     sssss    hhhhhhhhhh


TARGET    148   LSGLPKNRVI GSGTNLDSSR FRFLMSQRLG VAPTSCHGWI IGEHGDSSVP
4aj2D     149   isgfpknrvi gsgcnldsar frylmgerlg vhplschgwv lgehgdssvp
                                                                      
TARGET          hh     sss ss  hhhhhh hhhhhhhhh          ss s       ss
4aj2D           hh     sss ss  hhhhhh hhhhhhhhh          ss s       ss


TARGET    198   VWSGVNIAGV RLRELNPILG TGEDPEKWNE LHKQVVDSAY EVIKLKGYTS
4aj2D     199   vwsgvnvagv slkslnpqlg tdadkeqwkd vhkqvvdsay eviklkgyts
                                                                      
TARGET          s            hhh              hh hhhhhhhhhh hhhhh     
4aj2D           s            hhh              hh hhhhhhhhhh hhhhh     


TARGET    248   WAIGLSTASL ASAILRNTSS VAAVSTSVLG EHGIDKDVFL SLPCVLNANG
4aj2D     249   waiglsvadl aesimknlrr vhpistmikg lygikedvfl svpcilgqng
                                                                      
TARGET          hhhhhhhhhh hhhhhh   s ss   sss          sss   sssss  s
4aj2D           hhhhhhhhhh hhhhhh   s ss   sss          sss   sssss  s


TARGET    298   VTSVVKQILT PTEVEQLQKS ANIMSDVQAG LKF                  
4aj2D     299   isdvvkvtlt pdeearlkks adtlwgiqke lqf-                 
                                                                      
TARGET          sssss      hhhhhhhhhh hhhhhhhh                        
4aj2D           sssss      hhhhhhhhhh hhhhhhhh

Quality 


Template's ligands section 
Ligands in the template: 52C: 1, MLI: 3. 
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 4aj2 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: 4aj2.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 0.546 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 4aj2C 4aj2B 4aj2A  
 Unfortunately, we were not able to built the model as TETRAMER. 
 Thus, the model was built as single chain.

Template Selection 
 - Start SMR-Pipeline for:3f7894ce492d6b1f6b31e92ca60401cb on BC2-cluster at Fri Feb 22 02:52:08
2013 


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

FATAL - No A3m 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

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -  ********************************************************************************
 - Oligomeric modeling of 4aj2D was not successful, fall back to monomeric modeling
 - building model based on 4aj2D (3-332) 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:3f7894ce492d6b1f6b31e92ca60401cb on BC2-cluster at Fri Feb 22 02:58:45
2013


Template Description
Match Chain SeqId

4ajo: RAT LDHA IN COMPLEX WITH 2-((4-(4-((3-((2-METHYL-1,3- BENZOTHIAZOL-6YL)AMINO)-3-OXO-PROPYL)AMINO)-4-OXO-BUTYL) PHENYL)METHYL)PROPANEDIOIC ACID
Solved by: X-RAY, Resolution: 1.96A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4ajoC 62%
[Model]
3-332 4ajoA 62%
[Model]
3-332 4ajoD 62%
[Model]
3-332 4ajoB 62%
[Model]

4ajj: RAT LDHA IN COMPLEX WITH 2-((3,4-DIMETHOXYPHENYL)METHYL)) PROPANEDIOIC ACID AND N-(2-METHYL-1,3-BENZOTHIAZOL-6-YL)-UREIDO-PROPANAMIDE
Solved by: X-RAY, Resolution: 1.75A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4ajjB 62%
[Model]
3-332 4ajjA 62%
[Model]
3-332 4ajjD 62%
[Model]
3-332 4ajjC 62%
[Model]

4aj1: RAT LDHA IN COMPLEX WITH N-(2-(METHYLAMINO)-1,3- BENZOTHIAZOL-6-YL)ACETAMIDE
Solved by: X-RAY, Resolution: 1.87A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4aj1D 62%
[Model]
3-332 4aj1C 62%
[Model]
3-332 4aj1B 62%
[Model]
3-332 4aj1A 62%
[Model]

4al4: RAT LDHA IN COMPLEX WITH 2-((4-(2-((3-((2-METHYL-1,3-BENZOYL)AMINO)3-OXO-PROPYL)CARBAMOYLAMINO)ETHOXY) PHENYL) METHYLPROPANEDIOIC ACID
Solved by: X-RAY, Resolution: 1.78A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4al4C 62%
[Model]
3-332 4al4B 62%
[Model]
3-332 4al4A 62%
[Model]
3-332 4al4D 62%
[Model]

4aj4: RAT LDHA IN COMPLEX WITH 4-((2-ALLYLSULFANYL-1,3-BENZOTHIZAMINO)-4-OXO-BUTANOIC ACID
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4aj4A 62%
[Model]
3-332 4aj4D 62%
[Model]
3-332 4aj4C 62%
[Model]
3-332 4aj4B 62%
[Model]

4aji: RAT LDHA IN COMPLEX WITH 2-((3,4-DIMETHOXYPHENYL)METHYL)) PROPANEDIOIC ACID
Solved by: X-RAY, Resolution: 1.93A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4ajiD 62%
[Model]
3-332 4ajiC 62%
[Model]
3-332 4ajiB 62%
[Model]
3-332 4ajiA 62%
[Model]

4ajh: RAT LDHA IN COMPLEX WITH N-(2-METHYL-1,3-BENZOTHIAZOL-6-YLPROPANAMIDE AND 2-(4-BROMOPHENOXY)PROPANEDIOIC ACID
Solved by: X-RAY, Resolution: 1.93A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4ajhD 62%
[Model]
3-332 4ajhC 62%
[Model]
3-332 4ajhB 62%
[Model]
3-332 4ajhA 62%
[Model]

4ajn: RAT LDHA IN COMPLEX WITH 2-((4-(2-((3-((2-METHYL-1,3- BENZOTHIAZOL-6-YL)AMINO)-3-OXO-PROPYL)CARBAMOYLAMINO)ETHYPHENYL)METHYL)PROPANEDIOIC ACID
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4ajnD 62%
[Model]
3-332 4ajnB 62%
[Model]
3-332 4ajnC 62%
[Model]
3-332 4ajnA 62%
[Model]

4aje: RAT LDHA IN COMPLEX WITH 2-(4-BROMOPHENOXY)PROPANEDIOIC ACID
Solved by: X-RAY, Resolution: 2.35A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4ajeB 62%
[Model]
3-332 4ajeD 62%
[Model]
3-332 4ajeC 62%
[Model]
3-332 4ajeA 62%
[Model]

4ajl: RAT LDHA IN COMPLEX WITH 3-(ETHYLCARBAMOYLAMINO)-N-(2-METHBENZOTHIAZOL-6-YL)PROPANAMIDE
Solved by: X-RAY, Resolution: 1.77A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4ajlC 62%
[Model]
3-332 4ajlB 62%
[Model]
3-332 4ajlA 62%
[Model]
3-332 4ajlD 62%
[Model]

4aj2: RAT LDHA IN COMPLEX WITH 5-(2-CHLOROPHENYL)-1H-TETRAZOLE
Solved by: X-RAY, Resolution: 1.75A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4aj2A 62%
[Model]
3-332 4aj2C 62%
[Model]
3-332 4aj2B 62%
[Model]
3-332 4aj2D 62%
[Model]

4ajk: RAT LDHA IN COMPLEX WITH N-(2-(METHYLAMINO)-1,3-BENZOTHIAZACETAMIDE
Solved by: X-RAY, Resolution: 2.03A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-332 4ajkC 62%
[Model]
3-332 4ajkD 62%
[Model]
3-332 4ajkA 62%
[Model]
3-332 4ajkB 62%
[Model]

1i0z: HUMAN HEART L-LACTATE DEHYDROGENASE H CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-331 1i0zB 62%
[Model]
2-331 1i0zA 62%
[Model]

1t2f: HUMAN B LACTATE DEHYDROGENASE COMPLEXED WITH NAD+ AND 4- HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-332 1t2fA 62%
[Model]
2-332 1t2fD 62%
[Model]
2-332 1t2fC 62%
[Model]
2-332 1t2fB 62%
[Model]

5ldh: STRUCTURE OF THE ACTIVE TERNARY COMPLEX OF PIG HEART LACTATE DEHYDROGENASE WITH S-LAC-NAD AT 2.7 ANGSTROMS RESOLUTION
Solved by: X-RAY, Resolution: 2.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-331 5ldhB 61%
[Model]
2-331 5ldhA 61%
[Model]

1i10: HUMAN MUSCLE L-LACTATE DEHYDROGENASE M CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-332 1i10E 60%
[Model]
2-332 1i10A 60%
[Model]
2-332 1i10H 60%
[Model]
2-332 1i10D 60%
[Model]
2-332 1i10C 60%
[Model]
2-332 1i10F 60%
[Model]
2-332 1i10B 60%
[Model]

3h3f: RABBIT MUSCLE L-LACTATE DEHYDROGENASE IN COMPLEX WITH NADHAND OXAMATE
Solved by: X-RAY, Resolution: 2.38A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-332 3h3fA 60%
[Model]
2-332 3h3fD 60%
[Model]
2-332 3h3fC 60%
[Model]
2-332 3h3fB 60%
[Model]
2-332 3h3fH 60%
[Model]
2-332 3h3fG 60%
[Model]
2-332 3h3fF 60%
[Model]
2-332 3h3fE 60%
[Model]

9ldb: DESIGN AND SYNTHESIS OF NEW ENZYMES BASED ON THE LACTATE DEHYDROGENASE FRAMEWORK
Solved by: X-RAY, Resolution: 2.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-332 9ldbA 60%
[Model]
2-332 9ldbB 60%
[Model]

9ldt: DESIGN AND SYNTHESIS OF NEW ENZYMES BASED ON THE LACTATE DEHYDROGENASE FRAMEWORK
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-332 9ldtA 60%
[Model]
2-332 9ldtB 60%
[Model]

1v6a: CRYSTAL STRUCTURE OF L-LACTATE DEHYDROGENASE FROM CYPRINUSCARPIO
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-330 1v6aB 60%
[Model]
2-330 1v6aA 60%
[Model]

4ajp: HUMAN LDHA IN COMPLEX WITH 2-((4-(4-((3-((2-METHYL-1,3- BENZOTHIAZOL-6YL)AMINO)-3-OXO-PROPYL)AMINO)-4-OXO-BUTYL) PHENYL)METHYL)PROPANEDIOIC ACID
Solved by: X-RAY, Resolution: 2.38A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-332 4ajpB 60%
[Model]
2-332 4ajpA 60%
[Model]
2-332 4ajpC 60%
[Model]
2-332 4ajpD 60%
[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.