SWISS-MODEL Repository - Model Details

Model Overview
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1
1759

Sequence
UniProt P17139
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P17139: 6239.K04H4.1a

Domain
Link to: [ InterPro ]
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
Collagen
C4
C4

Model 3D Structure
Model information:
Modelled residue range: 1535 to 1757
Based on template: [ 1t60 ]  
Sequence Identity [%]: 66%
Model date: 2013-02-20
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1t60): HETERO HEXAMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: K: 1.
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          GFTFA KHSQTTAVPQ CPPGASQLWE GYSLLYVQGN GRASGQDLGQ
1t60G     2     vdh--gflvt rhsqttddpq cppgtkilyh gysllyvqgn erahgqdlgt
                                                                      
TARGET                ssss sss             sssss sssssssss   sssss    
1t60G                 ssss sss             sssss sssssssss   sssss    


TARGET    46    PGSCLSKFNT MPFMFCNMNS VCHVSSRNDY SFWLSTDEPM TPMMNPVTGT
1t60G     50    agsclrkfst mpflfcninn vcnfasrndy sywlstpepm pmsmapitge
                                                                      
TARGET            sss          sss    sss     ss ssssss               
1t60G             sss          sss    sss     ss ssssss               


TARGET    96    AIRPYISRCA VCEVPTQIIA VHSQDTSVPQ CPQGWSGMWT GYSFVMHTAA
1t60G     100   nirpfisrca vceapamvma vhsqtiqipq cptgwsslwi gysfvmhtsa
                                                                      
TARGET          hhhhssssss ssss  ssss sss           sssssss sssssssss 
1t60G           hhhhssssss ssss  ssss sss           sssssss sssssssss 


TARGET    146   GAEGTGQSLQ SPGSCLEEFR AVPFIECHGR GTCNYYATNH GFWLSIVDQD
1t60G     150   gaegsgqala spgscleefr sapfiechgr gtcnyyanay sfwlatiers
                                                                      
TARGET            sssss       sss       sssssss   sss     s ssssss  hh
1t60G             sssss       sss       sssssss   sss     s ssssss  hh


TARGET    196   KQFRKPMSQT LKAGGLKDRV SRCQVCLK -                      
1t60G     200   emfkkptpst lkagelrthv srcqvcmrrt                      
                                                                      
TARGET          h                  ss ssssssss                        
1t60G           h                  ss sssssssss                       



Quality


Template's ligands section
Ligands in the template: K: 1.
Ligands in the template that will be assessed: K5103.
Model's ligands section
K5103
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand K5103 will not be included in the final model.
K5103: conservation:False, RMSD:False, included: False

No ligands were included in the model.


Quaternary Structure Annotation of the Template
1t60 is annotated as HETERO HEXAMER
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: 1t60.pdb2.gz

Quaternary Structure Modelling of the Target Protein
1t60_2


Template Selection
 - Start SMR-Pipeline for:09a5c0744a2e2605f2bb1309fff072e8 on BC2-cluster at Wed Feb 20 12:34:55
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with C found
 - No template with F found
 - No template with I found
 - No template with L found
 - No template with C found
 - No template with F found
 - No template with C found
 - No template with F found
 - No template with I found
 - No template with L found
 - No template with O found
 - No template with R found
 - No template with U found
 - No template with X found
 - No template with C found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - Warning: Oligomer Prediction was not successfull!

 - 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 1t60G (1535-1757) 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:09a5c0744a2e2605f2bb1309fff072e8 on BC2-cluster at Wed Feb 20 12:37:21
2013 




Template Description
Match Chain SeqId

1t61: CRYSTAL STRUCTURE OF COLLAGEN IV NC1 DOMAIN FROM PLACENTA BASEMENT MEMBRANE
Solved by: X-RAY, Resolution: 1.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1536-1757 1t61B 67%
[Model]
1535-1757 1t61E 67%
[Model]
1535-1757 1t61D 67%
[Model]
1535-1757 1t61A 67%
[Model]

1li1: THE 1.9-A CRYSTAL STRUCTURE OF THE NONCOLLAGENOUS (NC1) DOMAIN OF HUMAN PLACENTA COLLAGEN IV SHOWS STABILIZATION VIA A NOVEL TYPE OF COVALENT MET-LYS CROSS-LINK
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1535-1757 1li1A 65%
[Model]
1535-1757 1li1D 65%
[Model]
1535-1757 1li1E 65%
[Model]
1535-1757 1li1B 65%
[Model]

1m3d: STRUCTURE OF TYPE IV COLLAGEN NC1 DOMAINS
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1536-1757 1m3dB 67%
[Model]
1535-1757 1m3dD 67%
[Model]
1535-1757 1m3dE 67%
[Model]
1535-1757 1m3dA 67%
[Model]
1535-1758 1m3dF 60%
[Model]
1536-1757 1m3dK 67%
[Model]
1535-1757 1m3dG 67%
[Model]
1535-1757 1m3dH 67%
[Model]
1535-1757 1m3dJ 67%
[Model]

1t60: CRYSTAL STRUCTURE OF TYPE IV COLLAGEN NC1 DOMAIN FROM BOVINE LENS CAPSULE
Solved by: X-RAY, Resolution: 1.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1535-1757 1t60B 67%
[Model]
1535-1757 1t60D 67%
[Model]
1535-1757 1t60E 67%
[Model]
1535-1757 1t60A 67%
[Model]
1535-1757 1t60H 67%
[Model]
1535-1757 1t60K 67%
[Model]
1535-1757 1t60J 67%
[Model]
1538-1758 1t60L 60%
[Model]
1536-1757 1t60N 67%
[Model]
1535-1757 1t60P 67%
[Model]
1535-1757 1t60Q 67%
[Model]
1535-1757 1t60M 67%
[Model]
1535-1758 1t60R 60%
[Model]
1535-1758 1t60O 60%
[Model]
1535-1757 1t60T 67%
[Model]
1535-1757 1t60S 67%
[Model]
1535-1757 1t60V 67%
[Model]
1535-1757 1t60W 67%
[Model]
1535-1758 1t60U 60%
[Model]
1535-1758 1t60X 60%
[Model]
1535-1757 1t60G 67%
[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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