SWISS-MODEL Repository - Model Details

Model Overview
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1
450

Sequence
UniProt P06603
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P06603: 7227.FBpp0081153

Domain
Link to: [ InterPro ]
Tubulin
Tubulin_C

Model 3D Structure
Model information:
Modelled residue range: 1 to 437
Based on template: [ 4f6r ]  
Sequence Identity [%]: 97%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (4f6r): HETERO TETRAMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: GTP: 1, SO4: 1.
Ligands in the model: GTP: 1
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       MRECISIH VGQAGVQIGN ACWELYCLEH GIQPDGQMPS DKTVGGGDDS
4f6rA     1       mrecisih vgqagvqign acwelycleh giqpdgqmps dktigggdds
                                                                      
TARGET                ssss sshhhhhhhh hhhhhhhhhh                      
4f6rA                 ssss sshhhhhhhh hhhhhhhhhh                      


TARGET    49    FNTFFSETGA GKHVPRAVFV DLEPTVVDEV RTGTYRQLFH PEQLITGKED
4f6rA     49    fntffsetga gkhvpravfv dleptvidev rtgtyrqlfh peqlitgked
                                                                      
TARGET          hhhsssss    sssssssss s   hhhhhh h            sssss   
4f6rA           hhhsssss    sssssssss s   hhhhhh h            sssss   


TARGET    99    AANNYARGHY TIGKEIVDLV LDRIRKLADQ CTGLQGFLIF HSFGGGTGSG
4f6rA     99    aannyarghy tigkeiidlv ldrirkladq ctglqgflvf hsfgggtgsg
                                                                      
TARGET              hhhhhh hhhhhhhhhh hhhhhhhhh       sssss sss  hhhhh
4f6rA               hhhhhh hhhhhhhhhh hhhhhhhhh       sssss sss  hhhhh


TARGET    149   FTSLLMERLS VDYGKKSKLE FAIYPAPQVS TAVVEPYNSI LTTHTTLEHS
4f6rA     149   ftsllmerls vdygkkskle fsiypapqvs tavvepynsi ltthttlehs
                                                                      
TARGET          hhhhhhhhhh hh    ssss ssss          hhhhhhh hhhhhh    
4f6rA           hhhhhhhhhh hh    ssss ssss          hhhhhhh hhhhhh    


TARGET    199   DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TASLRFDGAL
4f6rA     199   dcafmvdnea iydicrrnld ierptytnln rlisqivssi taslrfdgal
                                                                      
TARGET           ssssssshh hhhhhhhh        hhhhh hhhhhhhhh    hhh     
4f6rA            ssssssshh hhhhhhhh        hhhhh hhhhhhhhh    hhh     


TARGET    249   NVDLTEFQTN LVPYPRIHFP LVTYAPVISA EKAYHEQLSV AEITNACFEP
4f6rA     249   nvdltefqtn lvpyprihfp latyapvisa ekayheqlsv aeitnacfep
                                                                      
TARGET              hhhhhh            sssss  sss          h hhhhhh    
4f6rA               hhhhhh            sssss  sss          h hhhhhh    


TARGET    299   ANQMVKCDPR HGKYMACCML YRGDVVPKDV NAAIATIKTK RTIQFVDWCP
4f6rA     299   anqmvkcdpr hgkymaccll yrgdvvpkdv naaiatiktk rsiqfvdwcp
                                                                      
TARGET           sss         ssssssss ssss  hhhh hhhhhhhhhh           
4f6rA            sss         ssssssss ssss  hhhh hhhhhhhhhh           


TARGET    349   TGFKVGINYQ PPTVVPGGDL AKVQRAVCML SNTTAIAEAW ARLDHKFDLM
4f6rA     349   tgfkvginyq pptvvpggdl akvqravcml snttaiaeaw arldhkfdlm
                                                                      
TARGET             sssss           ss s  sssssss sssshhhhhh hhhhhhhhhh
4f6rA              sssss           ss s  sssssss sssshhhhhh hhhhhhhhhh


TARGET    399   YAKRAFVHWY VGEGMEEGEF SEAREDLAAL EKDYEEVGM            
4f6rA     399   yakrafvhwy vgegmeegef searedmaal ekdyeevgv-           
                                                                      
TARGET          hhh    hhh hh     hhh hhhhhhhhhh hhhhhh               
4f6rA           hhh    hhh hh     hhh hhhhhhhhhh hhhhhh

Quality 


Template's ligands section 
Ligands in the template: GTP: 1, SO4: 1. 
Ligands in the template that will be assessed: GTP501. 
Model's ligands section 
GTP501 
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: 0.060 
Given the properties calculated previously, the ligand A.GTP501 will be included in the model. 
GTP501: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 4f6r is annotated as HETERO 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: 4f6r.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 4f6r_1

Template Selection 
 - Start SMR-Pipeline for:0fb9a8ab497cf0cf80e8f3c8839dc65a on BC2-cluster at Thu Feb 21 17:56:32
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 B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with A found
 - No template with B found
 - No template with D found
 - No template with F found
 - No template with H found
 - No template with I found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with F found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with D found
 - No template with E 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 4f6rA (1-437) 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:0fb9a8ab497cf0cf80e8f3c8839dc65a on BC2-cluster at Thu Feb 21 17:57:55
2013


Template Description
Match Chain SeqId

4f6r: TUBULIN:STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 2.64A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-437 4f6rA 97%
[Model]

3j1u: LOW AFFINITY DYNEIN MICROTUBULE BINDING DOMAIN - TUBULIN C
Solved by: X-RAY, Resolution: 9.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-439 3j1uB 97%
[Model]

1tub: TUBULIN ALPHA-BETA DIMER, ELECTRON DIFFRACTION
Solved by: X-RAY, Resolution: 3.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-439 1tubA 97%
[Model]

3j1t: HIGH AFFINITY DYNEIN MICROTUBULE BINDING DOMAIN - TUBULIN
Solved by: X-RAY, Resolution: 9.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-439 3j1tB 97%
[Model]

4f61: TUBULIN:STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 4.17A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-439 4f61G 96%
[Model]
1-439 4f61C 96%
[Model]
1-439 4f61E 96%
[Model]

3hkd: TUBULIN-TN16 : RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 3.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-438 3hkdA 96%
[Model]
2-438 3hkdC 96%
[Model]

3ryf: GTP-TUBULIN: RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 2.52A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-438 3ryfA 97%
[Model]
1-439 3ryfC 96%
[Model]

3n2k: TUBULIN-NSC 613862: RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 4.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-438 3n2kA 96%
[Model]
2-438 3n2kC 96%
[Model]

3ryh: GMPCPP-TUBULIN: RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-439 3ryhA 97%
[Model]
1-439 3ryhC 96%
[Model]

3ut5: TUBULIN-COLCHICINE-USTILOXIN: STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 2.73A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-439 3ut5A 96%
[Model]
1-439 3ut5C 96%
[Model]

3hkc: TUBULIN-ABT751: RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 3.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-436 3hkcA 96%
[Model]
2-437 3hkcC 96%
[Model]

1sa1: TUBULIN-PODOPHYLLOTOXIN: STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 4.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 1sa1A 97%
[Model]
2-439 1sa1C 96%
[Model]

3n2g: TUBULIN-NSC 613863: RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 4.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-438 3n2gA 96%
[Model]
2-438 3n2gC 96%
[Model]

3ryi: GDP-TUBULIN: RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 2.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-438 3ryiA 97%
[Model]
1-438 3ryiC 96%
[Model]

3ryc: TUBULIN: RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-438 3rycA 96%
[Model]
1-439 3rycC 96%
[Model]

3hkb: TUBULIN: RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 3.65A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-438 3hkbC 96%
[Model]
2-437 3hkbA 96%
[Model]

1z2b: TUBULIN-COLCHICINE-VINBLASTINE: STATHMIN-LIKE DOMAIN COMPL
Solved by: X-RAY, Resolution: 4.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-437 1z2bA 96%
[Model]
2-437 1z2bC 96%
[Model]

4eb6: TUBULIN-VINBLASTINE: STATHMIN-LIKE COMPLEX
Solved by: X-RAY, Resolution: 3.47A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-439 4eb6A 96%
[Model]
1-439 4eb6C 96%
[Model]

3hke: TUBULIN-T138067: RB3 STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 3.60A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-437 3hkeA 96%
[Model]
2-438 3hkeC 96%
[Model]

4atx: RIGOR KINESIN MOTOR DOMAIN WITH AN ORDERED NECK-LINKER, DOCKED ON TUBULIN DIMER, MODELLED INTO THE 8A CRYO-EM MAPOF DOUBLECORTIN-MICROTUBULES DECORATED WITH KINESIN
Solved by: X-RAY, Resolution: 8.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 4atxB 95%
[Model]

2xrp: HUMAN DOUBLECORTIN N-DC REPEAT (1MJD) AND MAMMALIAN TUBULI(1JFF AND 3HKE) DOCKED INTO THE 8-ANGSTROM CRYO-EM MAP OFDOUBLECORTIN-STABILISED MICROTUBULES
Solved by: X-RAY, Resolution: 8.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 2xrpH 95%
[Model]
2-439 2xrpD 95%
[Model]
2-439 2xrpF 95%
[Model]
2-439 2xrpB 95%
[Model]

4atu: HUMAN DOUBLECORTIN N-DC REPEAT PLUS LINKER, AND TUBULIN (2DOCKED INTO AN 8A CRYO-EM MAP OF DOUBLECORTIN-STABILISED MICROTUBULES RECONSTRUCTED IN ABSENCE OF KINESIN
Solved by: X-RAY, Resolution: 8.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 4atuF 95%
[Model]
2-439 4atuB 95%
[Model]
2-439 4atuH 95%
[Model]
2-439 4atuD 95%
[Model]

4abo: MAL3 CH DOMAIN HOMOLOGY MODEL AND MAMMALIAN TUBULIN (2XRP)INTO THE 8.6-ANGSTROM CRYO-EM MAP OF MAL3-GTPGAMMAS-MICRO
Solved by: X-RAY, Resolution: 8.60A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-439 4aboF 95%
[Model]
3-439 4aboB 95%
[Model]
3-439 4aboH 95%
[Model]
3-439 4aboD 95%
[Model]

3du7: TUBULIN-COLCHICINE-PHOMOPSIN A: STATHMIN-LIKE DOMAIN COMPL
Solved by: X-RAY, Resolution: 4.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 3du7C 97%
[Model]
2-439 3du7A 95%
[Model]

3e22: TUBULIN-COLCHICINE-SOBLIDOTIN: STATHMIN-LIKE DOMAIN COMPLE
Solved by: X-RAY, Resolution: 3.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-436 3e22A 95%
[Model]
2-436 3e22C 94%
[Model]

4drx: GTP-TUBULIN IN COMPLEX WITH A DARPIN
Solved by: X-RAY, Resolution: 2.22A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-437 4drxA 96%
[Model]
2-437 4drxC 94%
[Model]

1sa0: TUBULIN-COLCHICINE: STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 3.58A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-437 1sa0A 96%
[Model]
2-437 1sa0C 94%
[Model]

1ffx: TUBULIN:STATHMIN-LIKE DOMAIN COMPLEX
Solved by: X-RAY, Resolution: 3.95A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-439 1ffxC 93%
[Model]
1-439 1ffxA 93%
[Model]

3dco: DROSOPHILA NOD (3DC4) AND BOVINE TUBULIN (1JFF) DOCKED INTTHE 11-ANGSTROM CRYO-EM MAP OF NUCLEOTIDE-FREE NOD COMPLEXED TO THE MICROTUBULE
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 3dcoA 92%
[Model]

3edl: KINESIN13-MICROTUBULE RING COMPLEX
Solved by: X-RAY, Resolution: 28.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-437 3edlF 94%
[Model]
2-439 3edlA 92%
[Model]

2wbe: KINESIN-5-TUBULIN COMPLEX WITH AMPPNP
Solved by: X-RAY, Resolution: 9.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 2wbeA 92%
[Model]

1jff: REFINED STRUCTURE OF ALPHA-BETA TUBULIN FROM ZINC-INDUCED SHEETS STABILIZED WITH TAXOL
Solved by: X-RAY, Resolution: 3.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 1jffA 92%
[Model]

2p4n: HUMAN MONOMERIC KINESIN (1BG2) AND BOVINE TUBULIN (1JFF) DOCKED INTO THE 9-ANGSTROM CRYO-EM MAP OF NUCLEOTIDE-FREEKINESIN COMPLEXED TO THE MICROTUBULE
Solved by: X-RAY, Resolution: 9.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 2p4nA 92%
[Model]

1tvk: THE BINDING MODE OF EPOTHILONE A ON A,B-TUBULIN BY ELECTROCRYSTALLOGRAPHY
Solved by: X-RAY, Resolution: 2.89A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 1tvkA 92%
[Model]

3iz0: HUMAN NDC80 BONSAI DECORATED MICROTUBULE
Solved by: X-RAY, Resolution: 8.60A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-439 3iz0A 92%
[Model]

4ffb: A TOG:ALPHA/BETA-TUBULIN COMPLEX STRUCTURE REVEALS CONFORMMECHANISMS FOR A MICROTUBULE POLYMERASE
Solved by: X-RAY, Resolution: 2.88A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-438 4ffbA 75%
[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.