SWISS-MODEL Repository 
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
Domain
Link to: [ InterPro ]
| WHEP-TRS | |
| WHEP-TRS | |
| WHEP-TRS | |
| WHEP-TRS | |
| WHEP-TRS | |
| WHEP-TRS | |
| tRNA-synt_2b | |
| tRNA-synt_1c | |
| HGTP_anticodon | |
| tRNA-synt_1c_C | |
| ProRS-C_1 |
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 LEATKEDN LPDWYSQVIT KGEMIEYYDV SGCYILRQWS FAIWKAIKTW
4hvc_1#1 1016 leakkeen ladwysqvit ksemieyhdi sgcyilrpwa yaiweaikdf
TARGET hhhhhhhhhh h sss ssshhh hhhhhhhhhh
4hvc_1#1 hhhhhhhhhh h sss ssshhh hhhhhhhhhh
TARGET 49 FDAEITRMGV KECYFPIFVS KAVLEKEKTH IADFAPEVAW VTKSGDSDLA
4hvc_1#1 1064 fdaeikklgv encyfpmfvs qsalekekth vadfapevaw vtrsgktela
TARGET hhhhhhhh sss sss hhhhh hhhh sss sssss sss
4hvc_1#1 hhhhhhhh sss sss hhhhh hhhh sss sssss sss
TARGET 99 EPIAVRPTSE TVMYPAYAKW VQSYRDLPIR LNQWNNVVRW EFKQPTPFLR
4hvc_1#1 1114 epiairptse tvmypayakw vqshrdlpik lnqwcnvvrw efkhpqpflr
TARGET ssss h hhhhhhhhhh ss sssssssss
4hvc_1#1 ssss h hhhhhhhhhh ss sssssssss
TARGET 149 TREFLWQEGH TAFADKEEAA KEVLDILDLY ALVYTHLLAI PVVKGRKTEK
4hvc_1#1 1164 treflwqegh safatmeeaa eevlqildly aqvyeellai pvvkgrktek
TARGET sssssssss sss hhhh hhhhhhhhhh hhhhhhh sssss
4hvc_1#1 sssssssss sss hhhh hhhhhhhhhh hhhhhhh sssss
TARGET 199 EKFAGGDYTT TVEAFISASG RAIQGATSHH LGQNFSKMFE IVYEDPETQ-
4hvc_1#1 1214 ekfaggdytt tieafisasg raiqggtshh lgqnfskmfe ivfedpkipg
TARGET sss sssssss s sssss ssss s hhhhhh sss
4hvc_1#1 sss sssssss s sssss ssss s hhhhhh sss
TARGET 248 QKKYVYQNSW GITTRTIGVM IMVHADNQGL VLPPHVACIQ AIVVPCGITV
4hvc_1#1 1264 ekqfayqnsw glttrtigvm tmvhgdnmgl vlpprvacvq vviipcgi--
TARGET ssssssss sssshhhhhh hhhh s ssssss
4hvc_1#1 ssssssss sssshhhhhh hhhh s ssssss
TARGET 298 NTKDDERAQL LDACKALEKR LVGGGVRCEG DYRDNYSPGW KFNHWELKGV
4hvc_1#1 1315 -lseedkeal iakcndyrrr llsvnirvra dlrdnyspgw kfnhwelkgv
TARGET hhhhhhh hhhhhhhhhh hh ssss s hhh hhhhhhhh
4hvc_1#1 hhhhhhh hhhhhhhhhh hh ssss s hhh hhhhhhhh
TARGET 348 PLRLEVGPKD LKAQQLVAVR RDTVEKITIP LADVEKKIPA LLETIHESML
4hvc_1#1 1364 pirlevgprd mkscqfvavr rdtgekltva eneaetklqa ilediqvtlf
TARGET ssssss hhh hhhsssssss s ssssss s hhhhhhh hhhhhhhhhh
4hvc_1#1 ssssss hhh hhhsssssss s ssssss s hhhhhhh hhhhhhhhhh
TARGET 398 NKAQEDMTSH TKKVTNWTDF CGFLEQKNIL LAPFCGEISC EDKIKADSAR
4hvc_1#1 1414 trasedlkth mvvantmedf qkildsgkiv qipfcgeidc edwikkttar
TARGET hhhhhhhhhh hhhh hhhhh s ssss hh hhhhhhh
4hvc_1#1 hhhhhhhhhh sss hhhh hhhhh ss ssss hh hhhhhhhhh
TARGET 448 GEEAEPGAPA MGAKSLCIPF DQPAPIAASD KCINPSCTNK PKFYTLFGRS
4hvc_1#1 1474 ---------- mgakslcipf kplcelqpga kcv----cnp akyytlfgrs
TARGET sss sss ssssss
4hvc_1#1 sss sss ssssss
TARGET 498 Y - GLEATK EDNLPDWYSQ VITKGEMIEY YDVSGCYILR QWSFAIWKAI
4hvc_1#1 1512 y---gleakk eenladwysq vitksemiey hdisgcyilr pwayaiweai
*
TARGET hhhhhhh hhhh sss sss hhhhhhhhhh
4hvc_1#1 hhhhhhh hhhh sss sss hhhhhhhhhh
TARGET 545 KTWFDAEITR MGVKECYFPI FVSKAVLEKE KTHIADFAPE VAWVTKSGDS
4hvc_1#1 1061 kdffdaeikk lgvencyfpm fvsqsaleke kthvadfape vawvtrsgkt
TARGET hhhhhhhhhh h sss s ss hhhh hhhh ssssssss s
4hvc_1#1 hhhhhhhhhh h sss s ss hhhhh hhhh ssssssss s
TARGET 595 DLAEPIAVRP TSETVMYPAY AKWVQSYRDL PIRLNQWNNV VRWEFKQPTP
4hvc_1#1 1111 elaepiairp tsetvmypay akwvqshrdl piklnqwcnv vrwefkhpqp
TARGET ss ssss hhhhhhhh hhh sssssssss ss
4hvc_1#1 ss ssss hhhhhhhh hhh sssssssss ss
TARGET 645 FLRTREFLWQ EGHTAFADKE EAAKEVLDIL DLYALVYTHL LAIPVVKGRK
4hvc_1#1 1161 flrtreflwq eghsafatme eaaeevlqil dlyaqvyeel laipvvkgrk
TARGET ssssss ssssss h hhhhhhhhhh hhhhhhhhhh sssss
4hvc_1#1 ssssss ssssss h hhhhhhhhhh hhhhhhhhhh sssss
TARGET 695 TEKEKFAGGD YTTTVEAFIS ASGRAIQGAT SHHLGQNFSK MFEIVYEDPE
4hvc_1#1 1211 tekekfaggd ytttieafis asgraiqggt shhlgqnfsk mfeivfedpk
TARGET ssssssssss ssssss s ssss hhhh h sssss
4hvc_1#1 ssssssssss ssssss s ssss hhhh hh sssss
TARGET 745 TQ-QKKYVYQ NSWGITTRTI GVMIMVHADN QGLVLPPHVA CIQAIVVPCG
4hvc_1#1 1261 ipgekqfayq nswglttrti gvmtmvhgdn mglvlpprva cvqvviipcg
TARGET sssssss ssssssshhh hhhhhhh sssssss
4hvc_1#1 sssssss ssssssshhh hhhhhhh sssssss
TARGET 794 ITVNTKDDER AQLLDACKAL EKRLVGGGVR CEGDYRDNYS PGWKFNHWEL
4hvc_1#1 1311 is----eedk ealiakcndy rrrllsvnir vradlrdnys pgwkfnhwel
TARGET hh hhhhhhhhhh hhhhh s ssss hhhhhhhhhh
4hvc_1#1 hhhh hhhhhhhhhh hhhhh s ssss hhhhhhhhhh
TARGET 844 KGVPLRLEVG PKDLKAQQLV AVRRDTVEKI TIPLADVEKK IPALLETIHE
4hvc_1#1 1361 kgvpirlevg prdmkscqfv avrrdtgekl tvaeneaetk lqailediqv
TARGET h ssssss hhhhhhssss ssss sss ssss hhhh hhhhhhhhhh
4hvc_1#1 h ssssss hhhhhhssss ssss sss ssss hhhh hhhhhhhhhh
TARGET 894 SMLNKAQEDM TSHTKKVTNW TDFCGFLEQK NILLAPFCGE ISCEDKIKAD
4hvc_1#1 1411 tlftrasedl kthmvvantm edfqkildsg kivqipfcge idcedwikkt
TARGET hhhhhhhhhh hhh sss h hhhhhhhh ssss hhhhhhhhhh
4hvc_1#1 hhhhhhhhhh hhh sss h hhhhhhhh ssssss hhhhhhhhhh
TARGET 944 SARGEEAEPG APAMGAKSLC IPFDQPAPIA ASDKCINPSC TNKPK-FYTL
4hvc_1#1 1461 t--------- --amgakslc ipfkplcelq pgakcv---c gknpakyytl
TARGET sss s ss sss sss ss
4hvc_1#1 h sss sss sss sss ssss
TARGET 993 FGRSY
4hvc_1#1 1508 fgrsy-
TARGET ss
4hvc_1#1 ss
Template's ligands section
Ligands in the template:ANP : 2,HFG : 2,MG : 2,ZN : 2.
Ligands in the template that will be assessed: ANP1, ANP125, MG127, MG3, ZN128, ZN4.
Model's ligands section
ANP1
ANP1 interacts, within a radius of 3 Angstroem, with the following ions: MG3. They will be considered as a single ligand.
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: 0.050
Given the properties calculated previously, the ligand z.ANP1 will be included in the model.
ANP1: conservation:True, RMSD:True, included: True
ANP125
ANP125 interacts, within a radius of 3 Angstroem, with the following ions: MG127. They will be considered as a single ligand.
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 z.ANP125 will be included in the model.
ANP125: conservation:True, RMSD:True, included: True
ZN4
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.ZN4 will not be included in the final model.
ZN4: conservation:False, RMSD:False, included: False
ZN128
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.ZN128 will not be included in the final model.
ZN128: conservation:False, RMSD:False, included: False
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
4hvc 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: 4hvc.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 0.792 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 4hvcA
Model was succesfully built as DIMER.
Template Selection
- Start SMR-Pipeline for:82ee64df93ce7356fc6057d5486f9aa5 on BC2-cluster at Thu Feb 21 14:37:05
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:
- Skip Template HHsearch issue
- Skip Template HHsearch issue
- No template with A found
- No template with A found
- No template with B found
- No template with B found
- No template with A found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:10): model based on new templates
- Send 10 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ***********************
- building model based on 4hvcB (1216-1714) was successful
- **
- building model based on 1fyjA (894-943) was successful
- **
- building model based on 1fyjA (748-797) was successful
- **
- building model based on 1fyjA (973-1022) was successful
- ***
- building model based on 1fyjA (816-872) was successful
- **
- building model based on 1d2dA (1048-1096) was successful
- ****************
- building model based on 2hz7A (195-530) was successful
- ***********************
- building model based on 2rd2A (195-688) was successful
- ******
- building model based on 4hi7A (42-163) was successful
- *******
- building model based on 4hz2A (2-159) 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:82ee64df93ce7356fc6057d5486f9aa5 on BC2-cluster at Thu Feb 21 15:20:04
2013
Template Search
| Template Description |
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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 BLAST |
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1fyj: SOLUTION STRUCTURE OF MULTI-FUNCTIONAL PEPTIDE MOTIF-1 PRESENT IN HUMAN GLUTAMYL-PROLYL TRNA SYNTHETASE (EPRS). Solved by: NMR, Identified by BLAST |
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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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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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4hi7: CRYSTAL STRUCTURE OF GLUTATHIONE TRANSFERASE HOMOLOG FROM MOJAVENSIS, TARGET EFI-501819, WITH BOUND GLUTATHIONE Solved by: X-RAY, Resolution: 1.25A, 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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4hz2: CRYSTAL STRUCTURE OF GLUTATHIONE S-TRANSFERASE XAUT_3756 (507152) FROM XANTHOBACTER AUTOTROPHICUS PY2 Solved by: X-RAY, Resolution: 1.50A, Identified by HHSEARCH |
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4hz4: CRYSTAL STRUCTURE OF GLUTATHIONE S-TRANSFERASE B4XH91 (TAR501787) FROM ACTINOBACILLUS PLEUROPNEUMONIAE Solved by: X-RAY, Resolution: 1.62A, Identified by HHSEARCH |
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2il3: STRUCTURES OF AN INSECT EPSILON-CLASS GLUTATHIONE S- TRANSFERASE FROM THE MALARIA VECTOR ANOPHELES GAMBIAE: EVIDENCE FOR HIGH DDT-DETOXIFYING ACTIVITY Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH |
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2imi: STRUCTURES OF AN INSECT EPSILON-CLASS GLUTATHIONE S- TRANSFERASE FROM THE MALARIA VECTOR ANOPHELES GAMBIAE: EVIDENCE FOR HIGH DDT-DETOXIFYING ACTIVITY Solved by: X-RAY, Resolution: 1.40A, Identified by HHSEARCH |
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2imk: STRUCTURES OF AN INSECT EPSILON-CLASS GLUTATHIONE S- TRANSFERASE FROM THE MALARIA VECTOR ANOPHELES GAMBIAE: EVIDENCE FOR HIGH DDT-DETOXIFYING ACTIVITY Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH |
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4ibp: CRYSTAL STRUCTURE OF A GLUTATHIONE TRANSFERASE FAMILY MEMBPSUEDOMONAS FLUORESCENS PF-5, TARGET EFI-900011, WITH BOUGLUTATHIONE Solved by: X-RAY, Resolution: 1.80A, Identified by HHSEARCH |
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4id0: CRYSTAL STRUCTURE OF A GLUTATHIONE TRANSFERASE FAMILY MEMBPSUEDOMONAS FLUORESCENS PF-5, TARGET EFI-900011, WITH BOUGLUTATHIONE SULFINIC ACID (GSO2H) AND ACETATE Solved by: X-RAY, Resolution: 1.10A, Identified by HHSEARCH |
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4hoj: CRYSTAL STRUCTURE OF GLUTATHIONE TRANSFERASE HOMOLOG FROM GONORRHOEAE, TARGET EFI-501841, WITH BOUND GLUTATHIONE Solved by: X-RAY, Resolution: 1.40A, Identified by HHSEARCH |
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4iel: CRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE FAMILY PRBURKHOLDERIA AMBIFARIA, TARGET EFI-507141, WITH BOUND GLU Solved by: X-RAY, Resolution: 1.60A, 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.