SWISS-MODEL Repository 
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SWISS-MODEL Repository - Model Details
Model Overview
Sequence
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
TARGET 1 EDKLDYVK SKIGEYPNFP KEGILFRDIF GALTDPKACV YLRDLLVDHI
1zn8_1#3 3 dselqlve qrirsfpdfp tpgvvfrdis pvlkdpasfr aaigllarhl
TARGET hhhhhhh sssss sssss h hhh hhhh hhhhhhhhhh
1zn8_1#3 hhhhhhh sssss sssss h hhh hhhh hhhhhhhhhh
TARGET 49 R-ESAPEAEV IVGLDSRGFL FNLLIATELG LGCAPIRKKG KLAGEVVSVE
1zn8_1#3 51 kathggridy iagldsrgfl fgpslaqelg lgcvlirkrg klpgptlwas
TARGET s sssss hhh hhhhhhhhh ssssssss ssssss
1zn8_1#3 hhh s sssss hhh hhhhhhhhh ssssssss ssssss
TARGET 98 YKLEYGIDTF ELQKSAIKPG QKVVVVDDLL ATGGSLVAAT ELIGKVGGVV
1zn8_1#3 101 ysleygkael eiqkdalepg qrvvvvddll atggtmnaac ellgrlqaev
TARGET sss sssss ssss ssssssssss hhhhhhh hhhhh ss
1zn8_1#3 sss sssss ssss ssssssssss hhhhhhh hhhhhh ss
TARGET 148 VESLVVMELV GLEGRKRL - ---------- -- AEDKLDY VKSKIGEYPN
1zn8_1#3 151 lecvslvelt slkgrekl-a pvpffsllqy e--adselql veqrirsfpd
*
TARGET ssss sss hhhhh hhhhh hh sssss
1zn8_1#3 ssssssssss hhhhh ssssssss hhhhh hh sssss
TARGET 183 FPKEGILFRD IFGALTDPKA CVYLRDLLVD HIR-ESAPEA EVIVGLDSRG
1zn8_1#3 19 fptpgvvfrd ispvlkdpas fraaigllar hlkathggri dyiagldsrg
TARGET sssss hhhh hh hhhhhhhhhh hh ssssss h
1zn8_1#3 sssss hhhh hh hhhhhhhhhh hhhhh ssssss h
TARGET 232 FLFNLLIATE LGLGCAPIRK KGKLAGEVVS VEYKLEYGID TFELQKSAIK
1zn8_1#3 69 flfgpslaqe lglgcvlirk rgklpgptlw asysleygka eleiqkdale
TARGET hhhhhhhhhh h sssssss s ssss sssss sss ssssss
1zn8_1#3 hhhhhhhhhh h sssssss s ssss sssss sss ssssss
TARGET 282 PGQKVVVVDD LLATGGSLVA ATELIGKVGG VVVESLVVME LVGLEGRKRL
1zn8_1#3 119 pgqrvvvvdd llatggtmna acellgrlqa evlecvslve ltslkgrekl
TARGET ssssssss ss hhhhh hhhhhhh ssssss ss s hhhh
1zn8_1#3 ssssssss ss hhhhh hhhhhhh ssssssssss ss hhhhh
TARGET --------- --
1zn8_1#3 169 apvpffsllq ye
TARGET
1zn8_1#3 sssssss s
Template's ligands section
Ligands in the template:AMP : 2,CL : 1.
Ligands in the template that will be assessed: AMP1, AMP178.
Model's ligands section
AMP1
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand z.AMP1 will not be included in the model.
AMP1: conservation:False, RMSD:False, included: False
AMP178
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand z.AMP178 will not be included in the model.
AMP178: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1zn8 is annotated as DIMER
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: 1zn8.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 (=DIMER)
The corresponding reliability score is 0.956 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1zn8A
Model was succesfully built as DIMER.
Template Selection
- Start SMR-Pipeline for:97bd98c0b40beb7f492ee97a48bd4306 on BC2-cluster at Thu Feb 21 09:47:08
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to 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
- 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 1zn8B (7-172) 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:97bd98c0b40beb7f492ee97a48bd4306 on BC2-cluster at Thu Feb 21 09:49:11
2013
Template Search
| Template Description |
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1hgx: HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE (HGXPRTASE) Solved by: X-RAY, Resolution: 1.90A, 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.