SWISS-MODEL Repository
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
| UniProt | P61168 |
Database: TrEMBL (Unreviewed)  |
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Domain
Model 3D Structure
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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 ]
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Alignment
3pbl_1#3 32 yalsycalil aivfgnglvc mavlkeralq tttnylvvsl avadllvatl
3pbl_1#3 hhhhhhhh hhhhhhhhhh hhhhh hhhhhhhhh hhhhhhhh
3pbl_1#3 82 vmpwvvylev tggvwnfsri ccdvfvtldv mmctasiwnl caisidryta
3pbl_1#3 hhhhhhhhh hh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh
3pbl_1#3 132 vvmpvhyqhg tgqsscrrva lmitavwvla favscpllfg fnttgdptvc
3pbl_1#3 h hhhhhh hhhh hhhhhhhhhh hhhhhhhh
3pbl_1#3 182 sisnpdfviy ssvvsfylpf gvtvlvyari yvvlkqrrrk nifemlride
3pbl_1#3 hhhhhh hhhhhhhhhh hhhhhhhhhh hhhhh hhhhhhhhh
3pbl_1#3 1012 glrlkiykdt egyytigigh lltkspslna akseldkaig rntngvitkd
3pbl_1#3 ssssss ssss s ss hh hhhhhhhh sss hh
3pbl_1#3 1062 eaeklfnqdv daavrgilrn aklkpvydsl davrraalin mvfqmgetgv
3pbl_1#3 hhhhhhhhhh hhhhhhhh hhhhhh hhhhhhhhhh hhh hhhh
3pbl_1#3 1112 agftnslrml qqkrwdeaav nlaksrwynq tpnrakrvit tfrtgtwday
3pbl_1#3 hhhhhhh h hhhhh hhh hhh hhhhhhhh hhhh
TARGET 1 KEKK ATQMLAIVLG VFIICWLPFF ITHILNIHCD CN-IPPVLYS
3pbl_1#3 319 gvpl--rekk atqmvaivlg afivcwlpff lthvlnthcq tchvspelys
TARGET hhh hhhhhhhhhh hhhhhhhhhh hhhhhhh hhhhh
3pbl_1#3 h hhhh hhh hhhh hhhhhhhhhh hhhhhhh hhhhh
TARGET 44 AFTWLGYVNS AVNPIIYTTF NIEFRKAFMK ILHC ----- ----------
3pbl_1#3 367 attwlgyvns alnpviyttf niefrkaflk ilsc-yalsy calilaivfg
TARGET hhhhhhhhhh hhhhhhhhh hhhhhhhh hh
3pbl_1#3 hhhhhhhhhh hhhhhhhhh hhhhhhhh hh hhh hhhhhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
3pbl_1#3 47 nglvcmavlk eralqtttny lvvslavadl lvatlvmpwv vylevtggvw
TARGET
3pbl_1#3 hhhhhhh hhhh hhhhhhhhhh hhhhhhhhhh hhhhh
TARGET ---------- ---------- ---------- ---------- ----------
3pbl_1#3 97 nfsriccdvf vtldvmmcta siwnlcaisi drytavvmps scrrvalmit
TARGET
3pbl_1#3 hhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhh hhhhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
3pbl_1#3 156 avwvlafavs cpllfgfntt gdptvcsisn pdfviyssvv sfylpfgvtv
TARGET
3pbl_1#3 hhhhhhhhhh hhhh hhhhhhhhhh hhhhhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
3pbl_1#3 206 lvyariyvvl kqrrrknife mlrideglrl kiykdtegyy tigighlltk
TARGET
3pbl_1#3 hhhhhhhhhh hhh hhh hhhhhh sss ss ss sss
TARGET ---------- ---------- ---------- ---------- ----------
3pbl_1#3 1036 spslnaakse ldkaigrntn gvitkdeaek lfnqdvdaav rgilrnaklk
TARGET
3pbl_1#3 hhhhhh hhhhh hhhhhh hhhhhhhhhh hhhh hhh
TARGET ---------- ---------- ---------- ---------- ----------
3pbl_1#3 1086 pvydsldavr raalinmvfq mgetgvagft nslrmlqqkr wdeaavnlak
TARGET
3pbl_1#3 hhhh hhh hhhhhhhhh hhhhh hhhhhh h hhhhhhhhh
TARGET 78 ---------- ---------- ---------- - KEKKATQM LAIVLGVFII
3pbl_1#3 1136 srwynqtpnr akrvittfrt gtwdaygvpl --rekkatqm vaivlgafiv
*
TARGET hhhhhhh hhhhhhhhhh
3pbl_1#3 hhh hh hhhhhhhhhh hhhhhhhh hhhhhhhhhh
TARGET 96 CWLPFFITHI LNIHC-DCNI PPVLYSAFTW LGYVNSAVNP IIYTTFNIEF
3pbl_1#3 341 cwlpfflthv lnthcqtchv spelysattw lgyvnsalnp viyttfnief
TARGET hhhhhhhhhh hhh hhhhhhhh hhhhh hh hhhhh hh
3pbl_1#3 hhhhhhhhhh hhh hhhhhhhh hhhhh hh hhhhh hh
TARGET 145 RKAFMKILHC
3pbl_1#3 391 rkaflkilsc -
TARGET hhhhhhh
3pbl_1#3 hhhhhh
Template's ligands section
Ligands in the template:MAL : 2.
Ligands in the template that will be assessed: MAL1, MAL2.
Model's ligands section
MAL1
There are not residues in the model that match the ones that interact with the ligand in the template.
Given the properties calculated previously, the ligand z.MAL1 will not be included in the model.
MAL1: conservation:False, RMSD:False, included: False
MAL2
There are not residues in the model that match the ones that interact with the ligand in the template.
Given the properties calculated previously, the ligand z.MAL2 will not be included in the model.
MAL2: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3pbl is annotated as DIMER
PISA was used to annotate the quaternary structure, because the author assignment was not complete
The template was built based on the following PISA annotation file: 3pbl_assembly.xml.gz
Quaternary Structure Modelling of the Target Protein
The quaternary structure can be assumed to be identical
To build the complex the following chains of the complex has been additionally identified: 3pblB
Model was succesfully built as DIMER.
Template Selection
- Start SMR-Pipeline for:3998bab1559c96a7b123c75bd8a2aac2 on BC2-cluster at Wed Feb 27 22:30:07
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 2
- But still uncovered regions of the target sequence detected, go for: HHSEARCH
FATAL - No A3m found
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with C found
- No template with B found
- No template with B found
- No template with C found
- No template with B found
- No template with C found
- No template with A found
- No template with B found
- No template with G found
- No template with N found
- No template with A found
- No template with B found
- No template with G found
- No template with N found
- No template with B found
- No template with B found
- No template with B found
- No template with A found
- No template with L found
- No template with H found
- No template with L found
- No template with H found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with C found
- No template with B found
- No template with C found
- No template with L found
- No template with H found
- No template with L found
- No template with H found
- No template with L found
- No template with H found
- No template with L found
- No template with H 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 3pblA (368-444) was successful
- **********************************
- building model based on 3pblA (37-222) was successful
- *******************
- building model based on 2ycyA (338-442) was successful
- ***************************************************************************
- building model based on 4eiyA (27-442) 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:3998bab1559c96a7b123c75bd8a2aac2 on BC2-cluster at Wed Feb 27 22:33:25
2013
Template Search
| Template Description |
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3pbl: STRUCTURE OF THE HUMAN DOPAMINE D3 RECEPTOR IN COMPLEX WITETICLOPRIDE Solved by: X-RAY, Resolution: 2.89A, Identified by BLAST |
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4grv: THE CRYSTAL STRUCTURE OF THE NEUROTENSIN RECEPTOR NTS1 IN NEUROTENSIN (8-13) Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH |
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2lnl: STRUCTURE OF HUMAN CXCR1 IN PHOSPHOLIPID BILAYERS Solved by: NMR, Identified by HHSEARCH |
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3vw7: CRYSTAL STRUCTURE OF HUMAN PROTEASE-ACTIVATED RECEPTOR 1 (WITH ANTAGONIST VORAPAXAR AT 2.2 ANGSTROM Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH |
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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.