SWISS-MODEL Repository - Model Details

Model Overview
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1
473

Sequence
UniProt Q09621
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q09621: 6239.ZK945.1

Domain
Link to: [ InterPro ]
Beta-lactamase

Model 3D Structure
Model information:
Modelled residue range: 103 to 181
Based on template: [ 1yqs ]  
Sequence Identity [%]: 37%
Model date: 2014-10-08
Revision date: 2014-10-06

Quaternary structure information: [details]
Template (1yqs): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: BSA: 2, GOL: 2.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment

TARGET    1                                           IVDLQ GGYADKASGR
1yqsA     3     lpapddtglq avlhtalsqg apgamvrvdd ngt--ihqls egvadratgr
                                                                      
TARGET                                                       ssss   ss
1yqsA                hhhhh hhhhhhhhh   sssssssss s s  sssss sssss   ss


TARGET    16    KWTPDTRTVV FSTTKAVGAV CVAMLVDRGH ISYDDKMSKI WPEFAQNGKE
1yqsA     51    aitttdrfrv gsvtksfsav vllqlvdegk ldldasvnty lpgllpd--d
                                                                      
TARGET          ss           hhhhhhhh hhhhhhhh          hhh           
1yqsA           ss     sss   hhhhhhhh hhhhhhhh          hhh           


TARGET    66    NITIDWLMSH RAGL ----- ---------- ---------- ----------
1yqsA     99    ritvrqvmsh rsglydytnd mfaqtvpgfe svrnkvfsyq dlitlslkhg
                                                                      
TARGET             hhhhh                                              
1yqsA              hhhhhh         hhh h   hhhhhh hh       h hhhhhhh   


TARGET          ---------- ---------- ---------- ---------- ----------
1yqsA     149   vtnapgaays ysntnfvvag mliekltghs vateyqnrif tplnltdtfy
                                                                      
TARGET                                                                
1yqsA                         h   hhh hhhhhhh    hhhhhhh    hhh       


TARGET          ---------- ---------- ---------- ---------- ----------
1yqsA     199   vhpdtvipgt hangyltpde aggalvdste qtvswaqsag avisstqdld
                                                                      
TARGET                                                                
1yqsA                         ssss         sss               sss hhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
1yqsA     249   tffsalmsgq lmsaaqlaqm qqwttvnstq gyglglrrrd lscgisvygh
                                                                      
TARGET                                                                
1yqsA           hhhhhhhh      hhhhhhh    sss  ss sss  sssss s   ssssss


TARGET          ---------- ---------- ---------- ---------- --------- 
1yqsA     299   tgtvqgyyty afaskdgkrs vtalantsnn vnvlntmart lesafcgkp 
                                                                      
TARGET                                                                
1yqsA           ssss sssss ssss   sss ssssssss   hhhhhhhhhh hhhhh     



Quality


Template's ligands section
Ligands in the template: BSA: 2, GOL: 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
1yqs 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: 1yqs.pdb1.gz

Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 37.975) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode

The target structure was calculated as SINGLE CHAIN


Template Selection
 - Start SMR-Pipeline for:fca9b26a69ff266221fd98030a31dfaf on BC2-cluster at Wed Oct  8 04:03:10
2014 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - No template with B found
 - No template with B found
 - No template with A found
 - No template with A found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:4): model based on new templates
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                  *************
 - building model based on 1yqsA (103-181) was successful 
 -                   ******************
 - building model based on 1o07B (109-215) was successful 
 -                   ***************************
 - building model based on 1i5qB (109-266) was successful 
 -             **************************************************************
 - building model based on 3zytA (68-434) 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:fca9b26a69ff266221fd98030a31dfaf on BC2-cluster at Wed Oct  8 04:05:48
2014 




Template Description
Match Chain SeqId

4k91: CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 5 (PBP5) FPSEUDOMONAS AERUGINOSA IN APO STATE
Solved by: X-RAY, Resolution: 2.05A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

99-155 4k91A 19%
[Model]
100-155 4k91B 20%
[Model]

4p87: CRYSTAL STRUCTURE OF EST-Y29, A NOVEL PENICILLIN-BINDING PLACTAMASE HOMOLOG FROM A METAGENOMIC LIBRARY
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

73-453 4p87A 13%
[Model]
74-453 4p87B 13%
[Model]

4p85: CRYSTAL STRUCTURE OF EST-Y29, A NOVEL PENICILLIN-BINDING PLACTAMASE HOMOLOG FROM A METAGENOMIC LIBRARY
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

73-453 4p85A 13%
[Model]
74-453 4p85B 13%
[Model]

4p6b: CRYSTAL STRUCTURE OF EST-Y29,A NOVEL PENICILLIN-BINDING PRLACTAMASE HOMOLOG FROM A METAGENOMIC LIBRARY
Solved by: X-RAY, Resolution: 1.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

73-453 4p6bA 12%
[Model]
74-453 4p6bB 12%
[Model]

3p09: CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM FRANCISELLA TULAR
Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

119-155 3p09B 11%
[Model]
91-155 3p09A 9%
[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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