SWISS-MODEL Repository 
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
Domain
Model 3D Structure
|
|
|
|
|||||||||||||||||||||||||||||||
|
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 ]
|
Alignment
TARGET 1 GHEKIKWE DEAAYEKEKR REGPGEWGKP VKLPEDKEVE KEALSLYKAN
2d7iA 68 gqklkdwh dkeairrdaq rvgngeqgrp ypmtdaervd qa----yren
TARGET sss hhhhhhhhh hhh
2d7iA sss hhhhhhhhh hhh
TARGET 49 GYNAYISDMI SLNRSIKDIR HKECKNMMYS AKLPTVSVIF PFHEEHNSTL
2d7iA 112 gfniyvsdki slnrslpdir hpncnskryl etlpntsiii pfhnegwssl
TARGET hhhhhh hhhh ss s ssssss ss hhhh
2d7iA hhhhhh hhhh ss s ssssss ss hhhh
TARGET 99 LRSVYSVINR SPPELLKEII LVDDFSEKPA LRQPLEDFLK KNKIDHIVKV
2d7iA 162 lrtvhsvlnr sppelvaeiv lvddfsdreh lkkpledyma ---lfpsvri
TARGET hhhhhhhhh sss ssss hhhhhhh ssss
2d7iA hhhhhhhhh sss ssss hhhhhhhh ssss
TARGET 149 LRTKKREGLI RGRQLGAQDA TGEILIFLDA HSEANYNWLP PLLDPIAEDY
2d7iA 209 lrtkkregli rtrmlgasva tgdvitflds hceanvnwlp plldriarnr
TARGET sss hh hhhhhhh ssssss sssss hh hhhhhhhh
2d7iA sss hh hhhhhhh ssssss sssss hh hhhhhhhh
TARGET 199 RTVVCPFVDV IDCETYEVRP QD-EGARGSF DWAFNYKRLP LTK-KDRESP
2d7iA 259 ktivcpmidv idhddfryet qagdamrgaf dwemyykrip ippelqkadp
TARGET sssss ssss ss sss ssss s sssss
2d7iA sssss ssss ss sss ssss s sssss
TARGET 247 TKPFNSPVMA GGYFAISAKW FWELGGYDEG LDIWGGEQYE LSFKVWQCHG
2d7iA 309 sdpfespvma gglfavdrkw fwelggydpg leiwggeqye isfkvwmcgg
TARGET sss ssssshh hhh hhhh hhhhhhh
2d7iA sss ssssshh hhh hhhh hhhhhhh
TARGET 297 RMVDAPCSRV AHIYRCKYAP FKNAGMGDFV SRNYKRVAEV WMDDYKETLY
2d7iA 359 rmedipcsrv ghiyr-kyvp yk-vpagvsl arnlkrvaev wmdeyaeyiy
TARGET sssss sss sss hhhhhhhhhh hhhhhh
2d7iA sssss sss sss hhhhhhhhhh hhhhhh
TARGET 347 KHRPGVGNAD AGDLKLMKGI REKLQCKSFD WFMKEIAFDQ DKYYPAVEPK
2d7iA 407 qrrpeyrhls agdvavqkkl rsslncksfk wfmtkiawdl pkfyppvepp
TARGET h hh hhhhhh hhh h hhhhh hh hhh
2d7iA hh hhhhhh hhh h hhhhh h h
TARGET 397 ASAEGEIRNV GTNFCIDTQF KEQNQRFGLR KCTSDDKDGG G------EQD
2d7iA 457 aaawgeirnv gtglcadtkh galgsplrle gcvr----gr geaawnnmqv
TARGET ssssssss ssss sss s
2d7iA ssssssss sss s
TARGET 441 LRLTRWHDIR PK----GRKI CFDCSTSVDK APVILFDCHS MKGNQLFKYR
2d7iA 503 ftftwredir pgdpqhtkkf cfdaisht-- spvtlydchs mkgnqlwkyr
TARGET ssss sss ss ss sss ssssssss sss
2d7iA ssss sss sss sssss sss sssss sss
TARGET 487 VAQKQIYHPI SGQCLTADEN GKGFLHMKKC DSSSDLQKWA WQTVDNELLE
2d7iA 551 -kdktlyhpv sgscmdcses dhr-ifmntc npssltqqwl fehtnstvle
TARGET sss sss ssss sss ss hhhh
2d7iA sss sss sss sss ss hhhh
TARGET 537 TRQAN
2d7iA 599 kfnrn-
TARGET
2d7iA
Template's ligands section
Ligands in the template:MN : 1,NAG : 3,NGA : 1,UDP : 1.
Ligands in the template that will be assessed: MN706, NAG700, NAG701, NAG704, UDP705.
Model's ligands section
NAG701
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand A.NAG701 will not be included in the model.
NAG701: conservation:False, RMSD:False, included: False
NAG704
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand A.NAG704 will not be included in the model.
NAG704: conservation:False, RMSD:False, included: False
UDP705
UDP705 interacts, within a radius of 3 Angstroem, with the following ions: MN706. 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 A.UDP705 will not be included in the model.
UDP705: conservation:False, RMSD:False, included: False
NAG700
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.NAG700 will not be included in the model.
NAG700: conservation:True, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2d7i 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: 2d7i.pdb1.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 0.288 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:5bf76bec516d39f23afce48c2ebf2a50 on BC2-cluster at Thu Feb 21 07:48:54
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:
- No template with B found
- No template with P 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 2d7iA (138-678) 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:5bf76bec516d39f23afce48c2ebf2a50 on BC2-cluster at Thu Feb 21 07:52:41
2013
Template Search
| Template Description |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
3kia: CRYSTAL STRUCTURE OF MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE RUBROBACTER XYLANOPHILUS Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
3o3p: CRYSTAL STRUCTURE OF R. XYLANOPHILUS MPGS IN COMPLEX WITH Solved by: X-RAY, Resolution: 2.53A, Identified by HHSEARCH |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
3vt0: CRYSTAL STRUCTURE OF CT1,3GAL43A IN COMPLEX WITH LACTOSE Solved by: X-RAY, Resolution: 3.19A, Identified by HHSEARCH |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
4hg6: STRUCTURE OF A CELLULOSE SYNTHASE - CELLULOSE TRANSLOCATIOINTERMEDIATE Solved by: X-RAY, Resolution: 3.25A, Identified by HHSEARCH |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
3vsf: CRYSTAL STRUCTURE OF 1,3GAL43A, AN EXO-BETA-1,3-GALACTANASCLOSTRIDIUM THERMOCELLUM Solved by: X-RAY, Resolution: 3.19A, Identified by HHSEARCH |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
3vt1: CRYSTAL STRUCTURE OF CT1,3GAL43A IN COMPLEX WITH GALACTOSE Solved by: X-RAY, Resolution: 3.19A, Identified by HHSEARCH |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
3vt2: CRYSTAL STRUCTURE OF CT1,3GAL43A IN COMPLEX WITH ISOPROPY-THIOGALACTOSIDE Solved by: X-RAY, Resolution: 3.19A, Identified by HHSEARCH |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
3vsz: CRYSTAL STRUCTURE OF CT1,3GAL43A IN COMPLEX WITH GALACTAN Solved by: X-RAY, Resolution: 3.19A, Identified by HHSEARCH |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
3f1y: MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM RUBROBACTER XYLANOPHILUS Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH |
|
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.