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Model Overview

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773

Sequence

UniProt

P33311

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

P33311: 4932.YPL270W

Domain

Link to: [ InterPro ]

	ABC_tran
	ABC_membrane

Model 3D Structure

	Model information:
	Modelled residue range:	443 to 675
	Based on template:	[ 3nha ]
	Sequence Identity [%]:	44%
	Model date:	2013-02-18
	Revision date:	2013-01-30

Quaternary structure information:	[details]
Template (3nha): MONOMER Model: MONOMER

Ligand information:	[details]
Ligands in the template: ADP: 1, BME: 2, MG: 1, PO4: 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                                               R GVIEFKDVSF
3nha_1#4  550   lvprgshmfi dmenmfdllk eetevkdlpg agplrfq--k griefenvhf
                                                                      
TARGET                                                       sssss    
3nha_1#4              hh    hhhhhhh                          sssss sss


TARGET    12    SYPTRPSVQI FKNLNFKIAP GSSVCIVGPS GRGKSTIALL LLRYYNPTTG
3nha_1#4  598   syadretlq- --dvsftvmp gqtlalvgps gagkstilrl lfrfydissg
                                                                      
TARGET                          sss    ssssss       hhhhhhh hh        
3nha_1#4               ss    s  sss    ssssss       hhhhhhh hh        


TARGET    62    TITIDNQDIS KLNCKSLRRH IGIVQQEPVL MSGTIRDNIT YGLTYTPTKE
3nha_1#4  646   ciridgqdis qvtqaslrsh igvvpqdtvl fndtiadnir ygrv-tagnd
                                                                      
TARGET          sssss sss     hhhhhh   sssss       ssshhhhh h       hh
3nha_1#4        sssss sss     hhhhhh   sssss       ssshhhhh h       hh


TARGET    112   EIRSVAKQCF CHNFITKFPN TYDTVIGPHG TLLSGGQKQR IAIARALIKK
3nha_1#4  695   eveaaaqaag ihdaimafpe gyrtqvgerg lklsggekqr vaiartilka
                                                                      
TARGET          hhhhhhhh    hhhhhh       sss         hhhhhh hhhhhhhhh 
3nha_1#4        hhhhhhh    hhhhhhh       sss         hhhhhh hhhhhhhhh 


TARGET    162   PTILILDEAT SALDVESEGA INYTFGQLMK SKSMTIVSIA HRLSTIRRSE
3nha_1#4  745   pgiilldeat saldtsnera iqaslakvca nr--ttivva hrlstvvnad
                                                                      
TARGET           sssssss       hhhhhh hhhhhhhhh      ssssss    hhhhh  
3nha_1#4         sssssss       hhhhhh hhhhhhhhh      ssssss    hhhhh  


TARGET    212   NVIVLGHDGS VVEMGKFKEL YA ------- -------              
3nha_1#4  793   qilvi-kdgc ivergrheal lsrggvyadm wqlqqgq              
                                                                      
TARGET          ssssss   s sssss hhhh hh                              
3nha_1#4        sssss s  s sssss hhhh hh   hhhhh hhhhh

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

Template's ligands section 
Ligands in the template: ADP: 1, BME: 2, MG: 1, PO4: 1. 
Ligands in the template that will be assessed: ADP2, MG3. 
Model's ligands section 
ADP2 
ADP2 interacts, within a radius of 3 Angstroem, with the following ions: MG3. They will be considered as a single ligand. 
One or more ligand's atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other ligands. 
Given the properties calculated previously, the ligand z.ADP2 will not be included in the model. 
ADP2: conservation:True, RMSD:False, included: False 
 
No ligands were included in the model.

Oligomer Modelling Log

Quaternary Structure Annotation of the Template 
 3nha 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: 3nha.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 (=MONOMER) 
 The corresponding reliability score is 0.54 (>0.5 indicates similarity) 
 Model was succesfully built as MONOMER.

Template Selection

 - Start SMR-Pipeline for:54ec35aa13d2f2b9581d35d0e2ad95b7 on BC2-cluster at Mon Feb 18 17:10:09
2013 


 - 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 modfied template library 
 - Summarize templates: 
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with D found
 - No template with A found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with E found
 - No template with G found
 - No template with F found
 - No template with A found
 - No template with B found
 - No template with E found
 - No template with F found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with E found
 - No template with F found
 - No template with A found
 - No template with B found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with E found
 - No template with G found
 - No template with F found
 - No template with E found
 - No template with F found
 - No template with A found
 - No template with B found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with A found
 - No template with B found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:3): model based on new templates
 - Send 3 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                               ************************
 - building model based on 3nhaA (443-675) was successful 
 -            ***********************************************************
 - building model based on 4aytA (107-672) was successful 
 -  *********
 - building model based on 4g1uD (9-91) 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:54ec35aa13d2f2b9581d35d0e2ad95b7 on BC2-cluster at Mon Feb 18 17:36:52
2013

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

4aby: CRYSTAL STRUCTURE OF DEINOCOCCUS RADIODURANS RECN HEAD DOMAIN
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

586-658	4abyA	15%	>target -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LSGGQKQRIAIARALI--KKPTILILDEATSALDVESEGAINYTFGQLMKSKSMTIVSIAHRLSTIRRSENVIVL---------------------------------------------- >4abyA PRLSRLEIRNLATITQLELELGGGFCAFTGETGAGKSIIVDALGLLLGGRANHDLIRSGEKELLVTGFWDSASRRLSSAGRGAARLSGEVVSVRELQEWAQGRLTIHWQHSAVSLLSPANQRGLLDRRVTKEAQAYAAAHAAWREAVSRLERLLVPRGSVDALHAELLKVGQALDAAREREAEPLVDSLLAVIRELGMPHARMEFALSALAEPAAYGLSDVLLRFSANPGEELGPLSDVASGGELSRVMLAVSTVLGADTPSVVFDEVDAGIGGAAAIAVAEQLSRLAD--TRQVLVVTHLAQIAARAHHHYKVEKQVEDGRTVSHVRLLTGDERLEEIARMLSGNTSEAALEHARELLA [Model]
586-658	4abyB	15%	>target ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LSGGQKQRIAIARAL--IKKPTILILDEATSALDVESEGAINYTFGQLMKSKSMTIVSIAHRLSTIRRSENVIVL-------------------------------------------- >4abyB PRLSRLEIRNLATITQLELELGGGFCAFTGETGAGKSIIVDALGLLLGGRANHDLIRSGEKELLVTGFWADSASRRLSSAGRGAARLSGEVVSVRELQEWAQGRLTIHWQHSAVSLLSPANQRGLLDRRVTKEAQAYAAAHAAWREAVSRLERLQATSLVPRGSVDALHAELLKVGQALDAAREREAEPLVDSLLAVIRELGMPHARMEFALSALAEPAAYGLSDVLLRFSANPGEELGPLSDVASGGELSRVMLAVSTVLGADTPSVVFDEVDAGIGGAAAIAVAEQLSRLAD--TRQVLVVTHLAQIAARAHHHYKVEKQVEDGRTVSHVRLLTGDERLEEIARMLSGNEAALEHARELLA [Model]
586-662	4abyC	15%	>target --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LSGGQKQRIAIAR--ALIKKPTILILDEATSALDVESEGAINYTFGQLMKSKSMTIVSIAHRLSTIRRSENVIVLGHDG-------------------------------------- >4abyC PRLSRLEIRNLATITQLELELGGGFCAFTGETGAGKSIIVDALGLLLGGRANHDLIRSGEKELLVTGFWGDESEDSASRRLSSAGRGAARLSGEVVSVRELQEWAQGRLTIHWQHSAVSLLSPANQRGLLDRRVTKEAQAYAAAHAAWREAVSRLEGSVDALHAELLKVGQALDAAREREAEPLVDSLLAVIRELGMPHARMEFALSALAEPAAYGLSDVLLRFSANPELGPLSDVASGGELSRVMLAVSTVLGADTPSVVFDEVDAGIGGAAAIAVAEQLSRLAD--TRQVLVVTHLAQIAARAHHHYKVEKQVTVSHVRLLTGDERLEEIARMLSGNTSEAALEHARELLA [Model]
584-664	4abyD	14%	>target -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TLLSGGQKQRI--AIARALIKKPTILILDEATSALDVESEGAINYTFGQLMKSKSMTIVSIAHRLSTIRRSENVIVLGHDGSV------------------------------- >4abyD PRLSRLEIRNLATITQLELELGGGFCAFTGETGAGKSIIVDALGLLLGGRANHDLIRELLVTGFWGADSASRRLSSAGRGAARLSGEVVSVRELQEWAQGRLTIHWQHSAVRGLLDRRVTKEAQAYAAAHAARGSVDALHAELLKVGQALDAAREREAEPLVDSLLAVIRELGMPHARMEFADVLLRFSANPEELGPLSDVASGGELSRVMLAVSTVLGADTPSVVFDEVDAGIGGAAAIAVAEQLSRLAD--TRQVLVVTHLAQIAARAHHHYKVEKQVETVSHVRLLTGDERLEEIARMLSSEAALEHARE [Model]
585-601	4abyD	44%	>target ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLSGGQKQRI-AIARALI---------- >4abyD PRLSRLEIRNLATITQLELELGGGFCAFTGETGAGKSIIVDALGLLLGGRANHDLIRELLVTGFWGADSASRRLSSAGRGAARLSGEVVSVRELQEWAQGRLTIHWQHSAVRGLLDRRVTKEAQAYAAAHAARGSVDALHAELLKVGQALDAAREREAEPLVDSLLAVIRELGMPHARMEFADVLLRFSANPEELGPLSDVASGGELSRVMLAVSTVLGADTPSVVFDEVDAGIGGAAAIAVAEQLSRLADTRQVLVVTHLAQIAARAHHHYKVEKQVETVSHVRLLTG--DERLEEIARMLSSEAALEHARE [Model]

4ad8: CRYSTAL STRUCTURE OF A DELETION MUTANT OF DEINOCOCCUS RADIRECN
Solved by: X-RAY, Resolution: 4.00A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

586-658

4ad8A

16%

[Model]

4g1u: X-RAY STRUCTURE OF THE BACTERIAL HEME TRANSPORTER HMUUV FRPESTIS
Solved by: X-RAY, Resolution: 3.01A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

443-685	4g1uC	24%	>target ----RGVIEFKDVSFSYPTRPSVQIFKNLNFKIAPGSSVCIVGPSGRGKSTIALLLLRYYNPTTGTITIDNQDISKLNCKSLRRHIGIVQQEPVL-MSGTIRDNITYGLT-Y--TPTKEEIRSVAKQCFCHNFITKFPNTYDTVIGPHGTLLSGGQKQRIAIARALIK------KPTILILDEATSALDVESEGAINYTFGQLMKSKSMTIVSIAHRLSTIR-RSENVIVLGHDGSVVEMGKFKELYANPTSALSQLL--------------------- >4g1uC AVTPVALLEASHLHYHVQQ---QALINDVSLHIASGEMVAIIGPNGAGKSTLLRLLTGYLSPSHGECHLLGQNLNSWQPKALARTRAVMRQYSELAFPFSVSEVIQMGRAPYGGSQDRQALQQVMAQTDCLALAQRD-----------YRVLSGGEQQRVQLARVLAQLWQPQPTPRWLFLDEPTSALDLYHQQHTLRLLRQLTRQEPLAVCCVLHDLNLAALYADRIMLL-AQGKLVACGTPEEVLNA--ETLTQWYQADLGVSRHPESALPQIYLRQ [Model]
445-685	4g1uD	23%	>target -VIEFKDVSFSYPTRPSVQIFKNLNFKIAPGSSVCIVGPSGRGKSTIALLLLRYYNPTTGTITIDNQDISKLNCKSLRRHIGIVQQEPV-LMSGTIRDNITYGLT---YTPTKEEIRSVAKQCFCHNFITKFPNTYDTVIGPHGTLLSGGQKQRIAIARALIK------KPTILILDEATSALDVESEGAINYTFGQLMKSKSMTIVSIAHRLSTIR-RSENVIVLGHDGSVVEMGKFKELYANPTSALSQLL--------------------- >4g1uD ALLEASHLHYHVQQ---QALINDVSLHIASGEMVAIIGPNGAGKSTLLRLLTGYLSPSHGECHLLGQNLNSWQPKALARTRAVMRQYSELAFPFSVSEVIQMGRAPYGGSQDRQALQQVMAQTDCLALAQR-----------DYRVLSGGEQQRVQLARVLAQLWQPQPTPRWLFLDEPTSALDLYHQQHTLRLLRQLTRQEPLAVCCVLHDLNLAALYADRIMLL-AQGKLVACGTPEEVLNA--ETLTQWYQADLGVSRHPESALPQIYLRQ [Model]
10-90	4g1uC	12%	>target ------------------------------------------------------------------------------------------------------------------------------------------------RLGICRNMLS------RPRLAKLPSIRFRSLVTPSSSQLIPLSRLCLRSP--AVGKSLILQSFRCNSSK-TVPETSLPSASPISKGSARS--------------------------------- >4g1uC AVTPVALLEASHLHYHVQQQALINDVSLHIASGEMVAIIGPNGAGKSTLLRLLTGYLSPSHGECHLLGQNLNSWQPKALARTRAVMRQYSELAFPFSVSEVIQMGRAPYGGSQDRQALQQVMAQTDCLALAQRDYRVLSGGEQQRVQLARVLAQLWQPQPTPRWLFLDEP--TSALDLYHQQHTLR---LLRQLTRQEPLAVCCVLHDLNLAALYADRIMLLAQGKLVACGTPEEVLNAETLTQWYQADLGVSRHPESALPQIYLRQ [Model]
9-91	4g1uD	13%	>target ------------------------------------------------------------------------------------------------------------------------------------------LRLGICRNMLS------RPRLAKLPSIRFRSLVTPSSSQLIPLSRLCLRSP--AVGKSLILQSFRCNSSK-TVPETSLPSASPISK-GSARSA------------------------------- >4g1uD ALLEASHLHYHVQQQALINDVSLHIASGEMVAIIGPNGAGKSTLLRLLTGYLSPSHGECHLLGQNLNSWQPKALARTRAVMRQYSELAFPFSVSEVIQMGRAPYGGSQDRQALQQVMAQTDCLALAQRDYRVLSGGEQQRVQLARVLAQLWQPQPTPRWLFLDEP--TSALDLYHQQHTLR---LLRQLTRQEPLAVCCVLHDLNLAALYADRIMLLAQGKLVACGTPEEVLNAETLTQWYQADLGVSRHPESALPQIYLRQ [Model]

Downloads

download model.tgz

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.