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 LA RGVINWGAPV SNLLEDGMLY VQQAKAPESS GLVSVLVAGA
1d2n_1#5 505 edyasy--im ngiikwgdpv trvlddgell vqqtknsdrt plvsvllegp
TARGET hh hhhhhhhhhh hhhhh sssssssss
1d2n_1#5 hhh hh hhhhhhhhhh hhhhhh sssssssss
TARGET 43 PNSGKTALAA QLAKMSDFPF VKVCSPEDMV GYTESAKCLH IRKIFDDAYR
1d2n_1#5 553 phsgktalaa kiaeesnfpf ikicspdkmi gfsetakcqa mkkifddayk
TARGET hhhhhh hhhhh s ssss hhhhhhh hhhhhhhhh
1d2n_1#5 hhhhhh hhhhh s ssss hhhhhhh hhhhhhhhh
TARGET 93 SMLSCIVVDN VERLLDYGSI GPRYSNMTLQ ALLVLLKKQP PKGRKLLILC
1d2n_1#5 603 sqlscvvvdd ierlldyvpi gprfsnlvlq allvllkkap pqgrklliig
TARGET sssssssss hhhhh hhhhh hhhhhhh ssssss
1d2n_1#5 sssssssss hhhhh hhhhh hhhhhhh ssssss
TARGET 143 TSSRREVLEE MEMLTAFTSV LHVPNLSKPD HVLAVLENTD IFSKGEIQAI
1d2n_1#5 653 ttsrkdvlqe memlnafstt ihvpniatge qllealellg nfkdkertti
TARGET ss hhhhh hhh ss sss hh hhhhhhhhh hhhhhhh
1d2n_1#5 ss hhhhh hhh ss sss hh hhhhhhhhh hhhhhhh
TARGET 193 GKKMAGKRVF IGIKKLLGLI DMARQTEQSQ RAIKFLSKME EEGG -----
1d2n_1#5 703 aqqvkgkkvw igikkllmli emslqmdpey rvrkflallr eega-splde
TARGET hhh hhhhhhhh hhhh h hhhhhhhhh h
1d2n_1#5 hhh hhhhhhhh hhhh hhhhhhhhhh h
TARGET 237 ------ LAR GVINWGAPVS NLLEDGMLYV QQAKAPESSG LVSVLVAGAP
1d2n_1#5 506 dyasy--imn giikwgdpvt rvlddgellv qqtknsdrtp lvsvllegpp
*
TARGET hhh hhhhhhhhhh hhhh s ssssssss
1d2n_1#5 hhh hhh hhhhhhhhhh hhhhh s ssssssss
TARGET 280 NSGKTALAAQ LAKMSDFPFV KVCSPEDMVG YTESAKCLHI RKIFDDAYRS
1d2n_1#5 554 hsgktalaak iaeesnfpfi kicspdkmig fsetakcqam kkifddayks
TARGET hhhhhhh hhhh ss sss hhhhhhhh hhhhhhhh
1d2n_1#5 hhhhhhh hhhh ss sss hhhhhhhh hhhhhhhh
TARGET 330 MLSCIVVDNV ERLLDYGSIG PRYSNMTLQA LLVLLKKQPP KGRKLLILCT
1d2n_1#5 604 qlscvvvddi erlldyvpig prfsnlvlqa llvllkkapp qgrklliigt
TARGET sssssssssh hhhh hhhhhh hhhhhh sssssss
1d2n_1#5 sssssssssh hhhh hhhhhh hhhhhh sssssss
TARGET 380 SSRREVLEEM EMLTAFTSVL HVPNLSKPDH VLAVLENTDI FSKGEIQAIG
1d2n_1#5 654 tsrkdvlqem emlnafstti hvpniatgeq llealellgn fkdkerttia
TARGET s hhhhh hhh sss ss hhh hhhhhhhh hhhhhhhh
1d2n_1#5 s hhhhh hhh sss ss hhh hhhhhhhh hhhhhhhh
TARGET 430 KKMAGKRVFI GIKKLLGLID MARQTEQSQR AIKFLSKMEE EGG ------
1d2n_1#5 704 qqvkgkkvwi gikkllmlie mslqmdpeyr vrkflallre ega-splded
TARGET hh hhhhhhhhh hhh h hhhhhhhhhh
1d2n_1#5 hh hhhhhhhhh hhh h hhhhhhhhhh
TARGET 473 ----- LARG VINWGAPVSN LLEDGMLYVQ QAKAPESSGL VSVLVAGAPN
1d2n_1#5 507 yasy--imng iikwgdpvtr vlddgellvq qtknsdrtpl vsvllegpph
*
TARGET hhhh hhhhhhhhhh hhh ss sssssss
1d2n_1#5 hhh hhhh hhhhhhhhhh hhhh ss sssssss
TARGET 517 SGKTALAAQL AKMSDFPFVK VCSPEDMVGY TESAKCLHIR KIFDDAYRSM
1d2n_1#5 555 sgktalaaki aeesnfpfik icspdkmigf setakcqamk kifddayksq
TARGET hhhhhhhh hhh sss ss hhhhhhhhh hhhhhhh s
1d2n_1#5 hhhhhhhh hhh sss ss hhhhhhhhh hhhhhhh s
TARGET 567 LSCIVVDNVE RLLDYGSIGP RYSNMTLQAL LVLLKKQPPK GRKLLILCTS
1d2n_1#5 605 lscvvvddie rlldyvpigp rfsnlvlqal lvllkkappq grklliigtt
TARGET sssssssshh hhh hhhhhhh hhhhh ssssssss
1d2n_1#5 sssssssshh hhh hhhhhhh hhhhh ssssssss
TARGET 617 SRREVLEEME MLTAFTSVLH VPNLSKPDHV LAVLENTDIF SKGEIQAIGK
1d2n_1#5 655 srkdvlqeme mlnafsttih vpniatgeql lealellgnf kdkerttiaq
TARGET hhhhh hhh ssss s hhhh hhhhhhh hhhhhhhhh
1d2n_1#5 hhhhh hhh ssss s hhhh hhhhhhh hhhhhhhhh
TARGET 667 KMAGKRVFIG IKKLLGLIDM ARQTEQSQRA IKFLSKMEEE GG -------
1d2n_1#5 705 qvkgkkvwig ikkllmliem slqmdpeyrv rkflallree ga-spldedy
TARGET h hhhhhhhhhh hh h h hhhhhhhhh
1d2n_1#5 h hhhhhhhhhh hh hh hhhhhhhhh
TARGET 709 ---- LARGV INWGAPVSNL LEDGMLYVQQ AKAPESSGLV SVLVAGAPNS
1d2n_1#5 508 asy--imngi ikwgdpvtrv lddgellvqq tknsdrtplv svllegpphs
*
TARGET hhhhh hhhhhhhhhh hh sss ssssss
1d2n_1#5 hhh hhhhh hhhhhhhhhh hhh sss ssssss
TARGET 754 GKTALAAQLA KMSDFPFVKV CSPEDMVGYT ESAKCLHIRK IFDDAYRSML
1d2n_1#5 556 gktalaakia eesnfpfiki cspdkmigfs etakcqamkk ifddayksql
TARGET hhhhhhhhh hh ssss s hhhhhhhhhh hhhhhh ss
1d2n_1#5 hhhhhhhhh hh ssss s hhhhhhhhhh hhhhhh ss
TARGET 804 SCIVVDNVER LLDYGSIGPR YSNMTLQALL VLLKKQPPKG RKLLILCTSS
1d2n_1#5 606 scvvvddier lldyvpigpr fsnlvlqall vllkkappqg rklliigtts
TARGET ssssssshhh hh hhhhhhhh hhhh ssssssss
1d2n_1#5 ssssssshhh hh hhhhhhhh hhhh ssssssss
TARGET 854 RREVLEEMEM LTAFTSVLHV PNLSKPDHVL AVLENTDIFS KGEIQAIGKK
1d2n_1#5 656 rkdvlqemem lnafsttihv pniatgeqll ealellgnfk dkerttiaqq
TARGET hhhhh h hh sssss hhhhh hhhhhh hhhhhhhhhh
1d2n_1#5 hhhhh h hh sssss hhhhh hhhhhh hhhhhhhhhh
TARGET 904 MAGKRVFIGI KKLLGLIDMA RQTEQSQRAI KFLSKMEEEG G --------
1d2n_1#5 706 vkgkkvwigi kkllmliems lqmdpeyrvr kflallreeg a-spldedya
TARGET h hhhhhhhhhh h h hh hhhhhhhh
1d2n_1#5 h hhhhhhhhhh h hhh hhhhhhhh h
TARGET 945 --- LARGVI NWGAPVSNLL EDGMLYVQQA KAPESSGLVS VLVAGAPNSG
1d2n_1#5 509 sy--imngii kwgdpvtrvl ddgellvqqt knsdrtplvs vllegpphsg
*
TARGET hhhhhh hhhhhhhhhh h ssss sssss
1d2n_1#5 hh hhhhhh hhhhhhhhhh hh ssss sssss
TARGET 991 KTALAAQLAK MSDFPFVKVC SPEDMVGYTE SAKCLHIRKI FDDAYRSMLS
1d2n_1#5 557 ktalaakiae esnfpfikic spdkmigfse takcqamkki fddayksqls
TARGET hhhhhhhhhh h sssss h hhhhhhhhhh hhhhh sss
1d2n_1#5 hhhhhhhhhh h sssss h hhhhhhhhhh hhhhh sss
TARGET 1041 CIVVDNVERL LDYGSIGPRY SNMTLQALLV LLKKQPPKGR KLLILCTSSR
1d2n_1#5 607 cvvvddierl ldyvpigprf snlvlqallv llkkappqgr klliigttsr
TARGET sssssshhhh h hhhhhhhhh hhh ssssssss
1d2n_1#5 sssssshhhh h hhhhhhhhh hhh ssssssss
TARGET 1091 REVLEEMEML TAFTSVLHVP NLSKPDHVLA VLENTDIFSK GEIQAIGKKM
1d2n_1#5 657 kdvlqememl nafsttihvp niatgeqlle alellgnfkd kerttiaqqv
TARGET hhhhh hh h sssss hhhhhh hhhhh h hhhhhhhhh
1d2n_1#5 hhhhh hh h sssss hhhhhh hhhhh h hhhhhhhhh
TARGET 1141 AGKRVFIGIK KLLGLIDMAR QTEQSQRAIK FLSKMEEEGG ---------
1d2n_1#5 707 kgkkvwigik kllmliemsl qmdpeyrvrk flallreega -spldedyas
TARGET hh hhhhhhhhhh h hhh hhhhhhh
1d2n_1#5 hh hhhhhhhhhh hhhh hhhhhhh hh
TARGET 1181 -- LARGVIN WGAPVSNLLE DGMLYVQQAK APESSGLVSV LVAGAPNSGK
1d2n_1#5 510 y--imngiik wgdpvtrvld dgellvqqtk nsdrtplvsv llegpphsgk
*
TARGET hhhhhhh hhhhhhhhhh sssss ssss h
1d2n_1#5 h hhhhhhh hhhhhhhhhh h sssss ssss h
TARGET 1228 TALAAQLAKM SDFPFVKVCS PEDMVGYTES AKCLHIRKIF DDAYRSMLSC
1d2n_1#5 558 talaakiaee snfpfikics pdkmigfset akcqamkkif ddayksqlsc
TARGET hhhhhhhhhh sssss hh hhhhhhhhhh hhhh ssss
1d2n_1#5 hhhhhhhhhh sssss hh hhhhhhhhhh hhhh ssss
TARGET 1278 IVVDNVERLL DYGSIGPRYS NMTLQALLVL LKKQPPKGRK LLILCTSSRR
1d2n_1#5 608 vvvddierll dyvpigprfs nlvlqallvl lkkappqgrk lliigttsrk
TARGET ssssshhhhh hhhhhhhhhh hh s sssssss h
1d2n_1#5 ssssshhhhh hhhhhhhhhh hh s sssssss h
TARGET 1328 EVLEEMEMLT AFTSVLHVPN LSKPDHVLAV LENTDIFSKG EIQAIGKKMA
1d2n_1#5 658 dvlqememln afsttihvpn iatgeqllea lellgnfkdk erttiaqqvk
TARGET hhhh hhh sssss hhhhhhh hhhh hh hhhhhhhh
1d2n_1#5 hhhh hhh sssss hhhhhhh hhhh hh hhhhhhhh
TARGET 1378 GKRVFIGIKK LLGLIDMARQ TEQSQRAIKF LSKMEEEGG ---
1d2n_1#5 708 gkkvwigikk llmliemslq mdpeyrvrkf lallreegas pld
TARGET hhh hhhhhhhhh h hhhh hhhhhh
1d2n_1#5 hhh hhhhhhhhh hhhhh hhhhhh
Template's ligands section
Ligands in the template:ANP : 6,GOL : 6,MG : 6.
Ligands in the template that will be assessed: ANP1098, ANP1372, ANP2, ANP276, ANP550, ANP824, MG1, MG1097, MG1371, MG275, MG549, MG823.
Model's ligands section
ANP2
ANP2 interacts, within a radius of 3 Angstroem, with the following ions: MG1. 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: 0.070
Given the properties calculated previously, the ligand z.ANP2 will be included in the model.
ANP2: conservation:True, RMSD:True, included: True
ANP276
ANP276 interacts, within a radius of 3 Angstroem, with the following ions: MG275. 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: 0.070
Given the properties calculated previously, the ligand z.ANP276 will be included in the model.
ANP276: conservation:True, RMSD:True, included: True
ANP550
ANP550 interacts, within a radius of 3 Angstroem, with the following ions: MG549. 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: 0.070
Given the properties calculated previously, the ligand z.ANP550 will be included in the model.
ANP550: conservation:True, RMSD:True, included: True
ANP824
ANP824 interacts, within a radius of 3 Angstroem, with the following ions: MG823. They will be considered as a single ligand.
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.ANP824 will not be included in the model.
ANP824: conservation:False, RMSD:False, included: False
ANP1098
ANP1098 interacts, within a radius of 3 Angstroem, with the following ions: MG1097. They will be considered as a single ligand.
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.ANP1098 will not be included in the model.
ANP1098: conservation:False, RMSD:False, included: False
ANP1372
ANP1372 interacts, within a radius of 3 Angstroem, with the following ions: MG1371. They will be considered as a single ligand.
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.ANP1372 will not be included in the model.
ANP1372: conservation:False, RMSD:False, included: False
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
1d2n is annotated as HEXAMER
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: 1d2n.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 (=HEXAMER)
The corresponding reliability score is 0.632 (>0.5 indicates similarity)
Model was succesfully built as HEXAMER.
Template Selection
- Start SMR-Pipeline for:1cebd2856ff208f54f5f9da651db31e4 on BC2-cluster at Fri Feb 22 09:03:06
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 A found
- No template with C found
- No template with E found
- No template with B found
- No template with D found
- No template with F found
- No template with A found
- No template with A found
- No template with A 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 A found
- No template with A found
- No template with C found
- No template with E found
- No template with B found
- No template with D found
- No template with F found
- No template with G found
- No template with H found
- No template with B found
- No template with A found
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:7): model based on new templates
- Send 7 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *************************
- building model based on 1d2nA (503-738) was successful
- *********************
- building model based on 1qcsA (5-200) was successful
- *********************
- building model based on 1lv7A (254-448) was not successful go to next best template
- **********************
- building model based on 3d8bA (254-456) was successful
- **************************
- building model based on 1s3sE (242-486) was successful
- *****************************
- building model based on 3hu3A (214-486) was successful
- ***************************************
- building model based on 1r7rA (242-608) was successful
- *******************************************
- building model based on 3cf2D (214-610) was successful
- ***********************************************
- building model based on 3cf1A (214-653) 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:1cebd2856ff208f54f5f9da651db31e4 on BC2-cluster at Fri Feb 22 09:37:09
2013
Template Search
| Template Description |
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3b85: CRYSTAL STRUCTURE OF PREDICTED PHOSPHATE STARVATION-INDUCEATPASE PHOH2 FROM CORYNEBACTERIUM GLUTAMICUM Solved by: X-RAY, Resolution: 2.35A, Identified by HHSEARCH |
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4gp6: POLYNUCLEOTIDE KINASE Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH |
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4gp7: POLYNUCLEOTIDE KINASE Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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2rh5: STRUCTURE OF APO ADENYLATE KINASE FROM AQUIFEX AEOLICUS Solved by: X-RAY, Resolution: 2.48A, Identified by HHSEARCH |
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3sr0: CRYSTAL STRUCTURE OF THE PHOSPHORYL TRANSFER TRANSITION STTHE ADENYLATE KINASE: ADP/ALF4/AMP IN THE ACTIVE SITE Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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2rgx: CRYSTAL STRUCTURE OF ADENYLATE KINASE FROM AQUIFEX AEOLICUIN COMPLEX WITH AP5A Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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4i1u: APO CRYSTAL STRUCTURE OF A DEPHOSPHO-COA KINASE FROM BURKHVIETNAMIENSIS Solved by: X-RAY, Resolution: 2.05A, Identified by HHSEARCH |
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4i1v: CRYSTAL STRUCTURE OF A DEPHOSPHO-COA KINASE FROM BURKHOLDEVIETNAMIENSIS BOUND TO ADP Solved by: X-RAY, Resolution: 2.60A, 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.