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 YTKPPLVIL SLDGFAREYV DRNI--VQTL
4gtwB 170 kswveetces idtpecpae- -fespptllf sldgfraeyl htwggllpvi
TARGET sssss sss hhh hh hh
4gtwB sssss sss hhh hh hhh
TARGET 28 NHIADCGVKA DKVYPSYPSK TFPNHYSIVT GLWPESHGIT DNSVFDPTIS
4gtwB 218 sklkncgtyt knxrpxyptk tfpnhysivt glypeshgii dnkxydpkxn
TARGET hhhhh sss hhhhhhhh sssss
4gtwB hhhhh sss hhhhhhhh sss
TARGET 78 PVLESMKSTK YEK----FFE GEPIWSVYKR KTGKKANCLF WVGCAYNNSG
4gtwB 268 asf-slksk- -ekfnplwyk gqpiw-vtan hqevksgtyf wpgsdveidg
TARGET sssss hh h
4gtwB sss hh hh hhhh h
TARGET 124 YAPDVAPAYN QELPFRNRID TVVEWLKLPV DERPGLITAY LHEPDNAGH-
4gtwB 314 ilpdiykvyn gsvpfeeril avlewlqlps herphfytly leepdssghs
TARGET hhhhh hhhhhh ssssss s hhhhh
4gtwB hhhhh hhhhhh ssssss s hhhhhh
TARGET 173 YQVDEEDVDE KLAEIDENLD YLMSRLSEEK LLECINFAIL SDHGMQLID-
4gtwB 364 hgpvssevik alqkvdrlvg xlxdglkdlg ldkclnlili sdhgxeqgsc
TARGET h hhhh hhhhhhhhhh hhhhhhhhh sssss s sss
4gtwB hhhh hhhhhhhhhh hhhhhhhhh sssss s sss
TARGET 222 -KTYYFQDYL D-LKGLITAK GVVGRVYI-- ---NDTTISV NDVVDKFRCK
4gtwB 414 kkyvylnkyl gdvnnvkvvy gpaarlrptd vpetyysfny ealaknlscr
TARGET ssss s sssss hhhhhh
4gtwB ssshhh ssssss s sssssss hhhhhhh
TARGET 265 IDTV--KTNT RSDVPTRKHY SRDPRVGEVL LEGRAGVTFY KSKADDY---
4gtwB 464 epnqhfrpyl kpflpkrlhf aksdri---- ----epltfy ldpqwqlaln
TARGET sss s sss s ss ssssh hhh
4gtwB ssssss s sssss ss sss
TARGET 310 ---ELSGDHG YDYFNPKMHT IFYARGPSFK QNTTISPYQN IQYMNLWMNL
4gtwB 506 psycgsgfhg sdnlfsnxqa lfigygpafk hgaevdsfen ievynlxcdl
TARGET sss sssss sss sss hhhhhhhhhh
4gtwB sss sssss sss sss hhhhhhhhhh
TARGET 357 LGIEGAVETN GTIGFFDNIL TNP---PRRD NPTNVIGECP MIAFPSVLKC
4gtwB 559 lglipa-pnn gshgslnhll kkpiynpshp keegflsqcp ikstsndlgc
TARGET h ss s
4gtwB h ss s sss
TARGET 404 S -------- ---------- ---------- ---------- ----------
4gtwB 608 tcdpdddiyh xtvpygrpri llkqhrvcll qqqqfltgys ldllxplwas
TARGET
4gtwB hhhh hh ss s ssssss ss ssssss s ssssss
TARGET ---------- ---------- ---------- ---------- ----------
4gtwB 675 ytflsndncl yqdlriplsp vhkcsyykls ygfltpprln hiyseallts
TARGET
4gtwB sss s ssss
TARGET ---------- ---------- ---------- ---------- ----------
4gtwB 741 nivpxyqsfq viwhylhdtl lqryaherng invvsgpvfd fdydgrydsl
TARGET
4gtwB sssss hhhh hhhhhhhhhh hhhhhhhh ssssssss h
TARGET ---------- ---------- ---------- ---------- ----------
4gtwB 791 eilkqnsrvi rsqeilipth ffivltsckq lsetplecsa lessayilph
TARGET
4gtwB hhhhh sss sss ss sssssssss s ssssssssss
TARGET ---------- ---------- ---------- ---------- ----------
4gtwB 841 rpdniescth gkresswvee lltlhrarvt dvelitglsf yqdrqesvse
TARGET
4gtwB hhhhhhh hhhhsss hh hhhhh sss hhh
TARGET ---------- --
4gtwB 891 llrlkthlpi fs
TARGET
4gtwB hhhhh
Template's ligands section
Ligands in the template:AMP : 1,CA : 1,NAG : 3,ZN : 2.
Ligands in the template that will be assessed: AMP1005, CA1008, NAG1001, NAG1003, NAG1004, ZN1006, ZN1007.
Model's ligands section
NAG1001
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand B.NAG1001 will not be included in the model.
NAG1001: conservation:False, RMSD:False, included: False
NAG1003
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand B.NAG1003 will not be included in the model.
NAG1003: conservation:False, RMSD:False, included: False
NAG1004
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand B.NAG1004 will not be included in the model.
NAG1004: conservation:False, RMSD:False, included: False
AMP1005
AMP1005 interacts, within a radius of 3 Angstroem, with the following ions: ZN1006, ZN1007. 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 B.AMP1005 will not be included in the model.
AMP1005: conservation:False, RMSD:False, included: False
CA1008
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 B.CA1008 will not be included in the final model.
CA1008: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
4gtw 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: 4gtw.pdb2.gz
Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.498 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:50fb04159483bc42f92ad57c093fb99a on BC2-cluster at Wed Feb 20 12:57:41
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:
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:2): model based on new templates
- Send 2 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ***************************************
- building model based on 4gtwB (177-580) was successful
- ****************************************************************
- Oligomeric modeling of 4gtwB was not successful, fall back to monomeric modeling
- building model based on 4gtwB (164-826) 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:50fb04159483bc42f92ad57c093fb99a on BC2-cluster at Wed Feb 20 13:07:52
2013
Template Search
| Template Description |
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4gtw: CRYSTAL STRUCTURE OF MOUSE ENPP1 IN COMPLEX WITH AMP Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH |
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4gtz: CRYSTAL STRUCTURE OF MOUSE ENPP1 IN COMPLEX WITH CMP Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH |
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4gtx: CRYSTAL STRUCTURE OF MOUSE ENPP1 IN COMPLEX WITH TMP Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH |
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4gty: CRYSTAL STRUCTURE OF MOUSE ENPP1 IN COMPLEX WITH GMP Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH |
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3ed4: CRYSTAL STRUCTURE OF PUTATIVE ARYLSULFATASE FROM ESCHERICHIA COLI Solved by: X-RAY, Resolution: 1.70A, Identified by HHSEARCH |
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1smn: IDENTIFICATION OF THE SERRATIA ENDONUCLEASE DIMER: STRUCTURAL BASIS AND IMPLICATIONS FOR CATALYSIS Solved by: X-RAY, Resolution: 2.04A, Identified by HHSEARCH |
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1ql0: SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT ATOMIC RESOLUTION Solved by: X-RAY, Resolution: 1.10A, Identified by HHSEARCH |
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1g8t: SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTI Solved by: X-RAY, Resolution: 2.04A, Identified by HHSEARCH |
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1qae: THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER Solved by: X-RAY, Resolution: 2.05A, 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.