SWISS-MODEL Repository - Model Details

Model Overview
Click on the bars to get more details about individual Models or experimental structures
1
333

Sequence
UniProt Q27888
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q27888: 6239.F13D12.2

Domain
Link to: [ InterPro ]
Ldh_1_N
Ldh_1_C

Model 3D Structure
Model information:
Modelled residue range: 38 to 333
Based on template: [ 1v6a ]  
Sequence Identity [%]: 62%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1v6a): TETRAMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: TRE: 2.
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                                               S ILQQNLANEL
1v6aB     1     astkeklith vskeepagpt nkvtvvgvgm vgmaaai--s illkdltdel
                                                                      
TARGET                                                      hhh      s
1v6aB             hhhhh                 sssss  h hhhhhhh  h hhh     ss


TARGET    12    CLVDVVADKL KGEMMDLQHG LAFTRHCTVK ADTDYSITAG SKLCVVTAGA
1v6aB     49    alvdvmedkl kgeamdlqhg slflkthkiv adkdysvtan skvvvvtaga
                                                                      
TARGET          ss    hhhh hhhhhhhh          sss ss   hh     sssss    
1v6aB           sss   hhhh hhhhhhhh    h     sss ss   hh     ssssss   


TARGET    62    RQREGETRLS LVQRNVEIFK GIIPQLVKYS PDTCILVVSN PVDVLTYVTW
1v6aB     99    rqqegesrln lvqrnvnifk fiipniikys pncillvvsn pvdiltyvaw
                                                                      
TARGET                 hhh hhhhhhhhhh hhhhhhhhh     sssss    hhhhhhhhh
1v6aB                  hhh hhhhhhhhhh hhhhhhhhh     sssss    hhhhhhhhh


TARGET    112   KLSGLPRERV FGSGTNLDSA RFRFLLSEKL NIAPSSCHGW IIGEHGDSSV
1v6aB     149   klsglprnrv igsgtnldsa rfrhlmgekl gihpsnchgw vigehgdssv
                                                                      
TARGET          hhh     ss sss  hhhhh hhhhhhhhhh          s ss       s
1v6aB           hh      ss sss  hhhhh hhhhhhhhhh          s ss       s


TARGET    162   AVWSGVNVAG VTLHEIKPDI GEKTDNEHWE AEIHKKVVDS AYEIIKLKGY
1v6aB     199   pvwsgvnvag vflqglnpdm gtdkdkedwk s-vhkmvvds ayeviklkgy
                                                                      
TARGET          ss            hhh                    hhh    hhhhhhh   
1v6aB           ss            hhh              h h hhhhh    hhhhhhh   


TARGET    212   TSWAIGLSVA KIAQGIFSNS RNVFALSTNV KGFHGINDDV YLSLPVVLGS
1v6aB     248   tswaigmsaa dlcqsilknl rkchpvstlv kgmhgvneev flsvpcilgn
                                                                      
TARGET            hhhhhhhh hhhhhhhh    sssssssss          s sssssssss 
1v6aB             hhhhhhhh hhhhhhhh    sssssssss          s sssssssss 


TARGET    262   AGLTHVVKQQ LTEAEVQKLH NSAKALLEVQ NGIVM                
1v6aB     298   sgltdvvhmt lksdeekqlv ksaetlwgvq kdltl-               
                                                                      
TARGET           ssssss      hhhhhhhh hhhhhhhhhh h                    
1v6aB            ssssss      hhhhhhhh hhhhhhhhhh h

Quality 


Template's ligands section 
Ligands in the template: TRE: 2. 
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 
 1v6a 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: 1v6a.pdb1.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 (=TETRAMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.388 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 1v6aA

Template Selection 
 - Start SMR-Pipeline for:cde79f2c5c6744902d169520d2f494a7 on BC2-cluster at Thu Feb 21 07:08:19
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 G 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 1v6aB (38-333) 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:cde79f2c5c6744902d169520d2f494a7 on BC2-cluster at Thu Feb 21 07:15:24
2013


Template Description
Match Chain SeqId

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

38-333 1v6aA 63%
[Model]
38-333 1v6aB 63%
[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 ]  

20-328 9ldbA 63%
[Model]
20-328 9ldbB 63%
[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 ]  

3-331 1t2fA 63%
[Model]
3-331 1t2fD 63%
[Model]
3-331 1t2fC 63%
[Model]
3-331 1t2fB 63%
[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 ]  

3-331 1i0zB 63%
[Model]
3-331 1i0zA 63%
[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 ]  

20-328 9ldtA 63%
[Model]
20-328 9ldtB 63%
[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 ]  

20-328 4aj1A 62%
[Model]
20-328 4aj1D 62%
[Model]
20-328 4aj1C 62%
[Model]
20-328 4aj1B 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 ]  

20-328 4ajhA 62%
[Model]
20-328 4ajhD 62%
[Model]
20-328 4ajhC 62%
[Model]
20-328 4ajhB 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 ]  

20-328 4ajlC 62%
[Model]
20-328 4ajlB 62%
[Model]
20-328 4ajlA 62%
[Model]
20-328 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 ]  

17-328 4aj2D 62%
[Model]
20-328 4aj2C 62%
[Model]
20-328 4aj2B 62%
[Model]
20-328 4aj2A 62%
[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 ]  

20-328 3h3fA 62%
[Model]
20-328 3h3fD 62%
[Model]
20-328 3h3fC 62%
[Model]
20-328 3h3fB 62%
[Model]
20-328 3h3fH 62%
[Model]
20-328 3h3fG 62%
[Model]
20-328 3h3fF 62%
[Model]
20-328 3h3fE 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 ]  

20-328 4ajiD 62%
[Model]
20-328 4ajiC 62%
[Model]
20-328 4ajiB 62%
[Model]
20-328 4ajiA 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 ]  

20-328 4aj4A 62%
[Model]
20-328 4aj4D 62%
[Model]
20-328 4aj4C 62%
[Model]
20-328 4aj4B 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 ]  

20-328 4ajeB 62%
[Model]
20-328 4ajeA 62%
[Model]
20-328 4ajeD 62%
[Model]
20-328 4ajeC 62%
[Model]

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 ]  

17-328 4ajoD 62%
[Model]
20-328 4ajoC 62%
[Model]
20-328 4ajoB 62%
[Model]
20-328 4ajoA 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 ]  

20-328 4ajkA 62%
[Model]
20-328 4ajkD 62%
[Model]
20-328 4ajkC 62%
[Model]
20-328 4ajkB 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 ]  

20-328 4ajnD 62%
[Model]
20-328 4ajnC 62%
[Model]
20-328 4ajnB 62%
[Model]
20-328 4ajnA 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 ]  

20-328 4al4C 62%
[Model]
20-328 4al4B 62%
[Model]
20-328 4al4A 62%
[Model]
20-328 4al4D 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 ]  

20-328 4ajjB 62%
[Model]
20-328 4ajjA 62%
[Model]
20-328 4ajjD 62%
[Model]
20-328 4ajjC 62%
[Model]

8ldh: REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

19-331 8ldhA 61%
[Model]

6ldh: REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

19-331 6ldhA 61%
[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 ]  

17-328 4ajpB 62%
[Model]
17-328 4ajpA 61%
[Model]
17-328 4ajpD 61%
[Model]
17-328 4ajpC 61%
[Model]

1ldm: REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

19-331 1ldmA 61%
[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 ]  

3-331 5ldhB 60%
[Model]
3-331 5ldhA 60%
[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 ]  

17-328 1i10A 61%
[Model]
17-328 1i10D 61%
[Model]
17-328 1i10C 61%
[Model]
17-328 1i10B 61%
[Model]
17-328 1i10E 61%
[Model]
17-328 1i10H 61%
[Model]
17-328 1i10F 61%
[Model]
17-328 1i10G 60%
[Model]

2v65: APO LDH FROM THE PSYCHROPHILE C. GUNNARI
Solved by: X-RAY, Resolution: 2.35A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

34-333 2v65A 60%
[Model]
34-333 2v65B 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.