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 GEC VTVQGWIRSV RSQKEVLFLH VN----DGSS
1x54A 1 miekvycqev kpeld--gkk vrlagwvytn mrvgkkiflw irdstgivqa
TARGET ss sssssss ss sss sssss s sss
1x54A ss ssssssssss sss sssss sss sssss
TARGET 30 LESLQIVADS SFDSR-ELTF GSSVQVQGQL VKSQSKRQNV ELKAEKIEVI
1x54A 49 vvaknvvgee tfekakklgr essvivegiv kaderapgga evhveklevi
TARGET ss h hhh s ssssssssss sss ss ssssssssss
1x54A ss h hhhhhh sssssssss sss ss ssssssssss
TARGET 79 GDCEAKAFPI K-YKERHPLE YLRQYPHLRC RTNALGSILR VRSEATAAIH
1x54A 99 q--avsefpi penpeqaspe llldyrhlhi rtpkasaimk vketlimaar
TARGET sss hh hhh hhhh hhhhhhh hhhhhhhhhh
1x54A hh hhh hhhh hhhhhhh hhhhhhhhhh
TARGET 128 SYFKDNGFVH IHTPVLTSND CEGAGELFQV EPSSKIKGPK ESFFDVPAFL
1x54A 147 ewllkdgwhe vfppilvtga veggatlfkl k--------- --yfdkyayl
TARGET hhhhhh ss s sss sss sss
1x54A hhhhhh ss s sss sss s s sssss
TARGET 178 TVSGQLHLEV MSGAFTQVFT FGPTFRAENS QSRRHLAEFY MVEAEISFVE
1x54A 186 sqsaqlylea aifglekvws ltpsfraeks rtrrhltefw hleleaawmd
TARGET s hhhhhh hhhh sssss ssssss ssss ssssssss
1x54A s hhhhhh hhhh sssss ssssss ssss ssssssss
TARGET 228 SLQDLMQVME ELFKATTEMV LSHCPEDVEL CHQFIAAGQK GRLEHMLKNN
1x54A 236 -lwdimkvee elvsymvqrt lelrkkeiem frddltt--- ------lknt
TARGET hhhhhhh hhhhhhhhhh hh hhhh hhhh
1x54A hhhhhhhhh hhhhhhhhhh hh hhhh hh hh
TARGET 278 ---FLIISYT EAIEILKQAS QNFAFTPKWG VDLQTEHEKY LVRHCGNIPV
1x54A 276 eppfprisyd eaidilqskg vnv----ewg ddlgadeerv lteef-drpf
TARGET sssssh hhhhhhhh hhhhhh hhhh s
1x54A sssssh hhhhhhhh hhhhhh hhh s
TARGET 325 FVINYPSELK PFYMRENEDG PQNTVAAVDL LVP-GVGELF GGSLREERYH
1x54A 321 fvygypkhik afymkedpnd prkvlas-dm lapegygeii ggsqreddyd
TARGET sss sss sssss ssssss ss ss ssss ssssss hh
1x54A sssssss sssss ssssss ss sss sssss ssssss hh
TARGET 374 VLEQRLARSG LT-KAYQWYL DLRKFGSVPH GGFGMGFERY LQCILGVDNI
1x54A 370 kllnrileeg mdpkdyewyl dlrrygsvph sgfglgverl vawvlkldhi
TARGET hhhhhhhh hhhh hh ss ssssssshhh hhhhh
1x54A hhhhhhhh hhhh hh ss ssssssshhh hhhhh
TARGET 423 KDVIPFPR - -----
1x54A 420 rwaalfprtp arlyp
TARGET hh
1x54A hh
Template's ligands section
Ligands in the template:4AD : 1,MG : 1,MPD : 1.
Ligands in the template that will be assessed: MG2000.
Model's ligands section
MG2000
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand MG2000 will not be included in the final model.
MG2000: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1x54 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: 1x54.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 0.922 (>0.5 indicates similarity)
Unfortunately, we were not able to built the model as DIMER.
Thus, the model was built as single chain.
Template Selection
- Start SMR-Pipeline for:bed8eb27f4b939c1fcd3945a2101a750 on BC2-cluster at Sat Feb 23 02:01:49
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 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 H found
- No template with I found
- No template with J 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
- 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
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ************************************************************************
- Oligomeric modeling of 1x54A was not successful, fall back to monomeric modeling
- building model based on 1x54A (41-470) 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:bed8eb27f4b939c1fcd3945a2101a750 on BC2-cluster at Sat Feb 23 02:25:52
2013
Template Search
| Template Description |
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4ah6: HUMAN MITOCHONDRIAL ASPARTYL-TRNA SYNTHETASE Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH |
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4ex5: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE LYSRS FROM BURKTHAILANDENSIS BOUND TO LYSINE Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH |
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4hvc: CRYSTAL STRUCTURE OF HUMAN PROLYL-TRNA SYNTHETASE IN COMPLHALOFUGINONE AND ATP ANALOGUE Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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3qne: CANDIDA ALBICANS SERYL-TRNA SYNTHETASE Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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3qo7: CRYSTAL STRUCTURE OF THE SERYL-TRNA SYNTHETASE FROM CANDID Solved by: X-RAY, Resolution: 2.55A, Identified by HHSEARCH |
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3qo5: CRYSTAL STRUCTURE OF THE SERYL-TRNA SYNTHETASE FROM CANDID Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH |
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3qo8: CRYSTAL STRUCTURE OF SERYL-TRNA SYNTHETASE FROM CANDIDA AL Solved by: X-RAY, Resolution: 2.00A, 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.