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 AGVLSRDA PDIESILALN PRVQAHATLR STAAKKLDKK HWKRNTDKNC
1h7w_2#2 2 apvlskdv adiesilaln prtqshaalh stlakkldkk hwkrnpdknc
TARGET hhhhh hhhhhhhhh h
1h7w_2#2 hhhhh hhhhhhhhh h
TARGET 49 FTCEKLESNF DDIKHTTLGE RGALREAVRC LKCADAPCQK SCPTSLDIKS
1h7w_2#2 50 fhceklennf ddikhttlge rgalreamrc lkcadapcqk scpthldiks
TARGET h hhhhhhhhh hhh h hhh
1h7w_2#2 h hhhhhhhhh hhhh h hhh
TARGET 99 FITSIANKNY YGAAKLIFSD NPLGLTCGMV CPTSDLCVGG CNLHAAEEGP
1h7w_2#2 100 fitsisnkny ygaakmifsd nplgltcgmv cptsdlcvgg cnlyateegs
TARGET hhhhh hh hhhhhhhhhh hhhhhh hh
1h7w_2#2 hhhhh hh hhhhhhhhhh hhhhhh hh
TARGET 149 INIGGLQQFA TEVFKAMNIP QIRNPSLPPP EHMPEAYSAK IALFGAGPAS
1h7w_2#2 150 inigglqqfa sevfkamnip qirnpclpsq ekmpeaysak iallgagpas
TARGET hhhhhhhh hhhhhh hh sssss hhh
1h7w_2#2 hhhhhhhh hhhhhh hh sssss hhh
TARGET 199 ISCASFLARL GYSNITIFEK QEYVGGLSTS EIPQFRLPYD VVNFEIELMK
1h7w_2#2 200 iscasflarl gysditifek qeyvgglsts eipqfrlpyd vvnfeielmk
TARGET hhhhhhhhhh ssssss hhhh h hhhhhhhhhh
1h7w_2#2 hhhhhhhhhh ssssss hhhh h hhhhhhhhhh
TARGET 249 DLGVKIICGK SLSTDEMTLS SLKENGYRAA FIGIGLPEPK KDHIFQGLTQ
1h7w_2#2 250 dlgvkiicgk slseneitln tlkeegykaa figiglpepk tddifqgltq
TARGET h sssss sss sss hh hhhhh ss sss sss
1h7w_2#2 h sssss sss sss hh hhhhh ss sss sss
TARGET 299 VQGFYTSKDF LPLVAKSSKT GMCACHSPLP SIRGAVIVLG AGDTAFDCAT
1h7w_2#2 300 dqgfytskdf lplvaksska gmcachsplp sirgavivlg agdtafdcat
TARGET ssssshhh hhhhhhhh ssssss hhhhhhhh
1h7w_2#2 ssssshhh hhhhhhhh ssssss hhhhhhhh
TARGET 349 SALRCGALRV FIVFRKGFVN IRAVPEEMEL AKEEKCEFLP FLSPRKVIVK
1h7w_2#2 350 salrcgarrv flvfrkgfvn iravpeevel akeekceflp flsprkvivk
TARGET hhhh ss ssss hhhhhh hh ssss ssssssssss
1h7w_2#2 hhhh ss ssss hhhhhh hh ssss ssssssssss
TARGET 399 DGKIVAMQFV RTEQDETGNW VEDEEQTVRL KADVVISAFG SVLEDPKVKE
1h7w_2#2 400 ggrivavqfv rteqdetgkw nededqivhl kadvvisafg svlrdpkvke
TARGET ssssssss sss sss sssss ss sssss s ss hhhhh
1h7w_2#2 ssssssss sss sss sssss ss sssss s ss hhhhh
TARGET 449 ALSPIKFNRW GLPEVNPETM QTSEPWVFAG GDVVGMANTT VESVNDGKQA
1h7w_2#2 450 alspikfnrw dlpevdpetm qtsepwvfag gdivgmantt vesvndgkqa
TARGET h sss sss s ss sssss h hhhhhhhhhh
1h7w_2#2 h sss sss s ss sssss h hhhhhhhhhh
TARGET 499 SWYIHKHIQA QYGTSVPSQP TMPLFYTPVD LVDISVEMAG LRFPNPFGLA
1h7w_2#2 500 swyihkyiqa qygasvsakp elplfytpvd lvdisvemag lkfinpfgla
TARGET hhhhhhhhhh h hh sss sss sssss
1h7w_2#2 hhhhhhhhhh h hh sss sss sssss
TARGET 549 SATPATSTPM IRRAFEAGWG FALTKTFSLD KDIVTNVSPR IIRGTTSGPL
1h7w_2#2 550 saapttsssm irrafeagwg faltktfsld kdivtnvspr ivrgttsgpm
TARGET hh hhhhhhh s ssss s ssss
1h7w_2#2 hh hhhhhhh s ssss s ssss
TARGET 599 YGPGQSSFLN IELISEKTAA YWCHSVTELK ADFPDNILIA SIMCSYNKSD
1h7w_2#2 600 ygpgqssfln ielisektaa ywcqsvtelk adfpdnivia simcsynknd
TARGET sssss s hh hhhhhhhhhh hh ssss ss hhh
1h7w_2#2 sssss s hh hhhhhhhhhh hh ssss ss hhh
TARGET 649 WMELSKMAEA SGADALELNL SCPHGMGERG MGLACGQDPE LVRNICRWVR
1h7w_2#2 650 wmelsrkaea sgadalelnl scphgmgerg mglacgqdpe lvrnicrwvr
TARGET hhhhhhhhhh sssss sss sss hh hhhhhhhhhh
1h7w_2#2 hhhhhhhhhh sssss sss sss hh hhhhhhhhh
TARGET 699 QAVRVPFFAK LTPNVTDIVS IARAAKEGGA DGVTATNTVS GLMGLKADGT
1h7w_2#2 700 qavqipffak ltpnvtdivs iaraakegga dgvtatntvs glmglkadgt
TARGET hh sssss s hh hhhhhhhh ssss ss s
1h7w_2#2 sssss s hh hhhhhhhh ssss ss s
TARGET 749 PWPAVGIGRR TTYGGVSGTA IRPIALRAVT AIARALPGFP ILATGGIDSA
1h7w_2#2 750 pwpavgagkr ttyggvsgta irpialravt tiaralpgfp ilatggidsa
TARGET ssssss hhhhhhhh hhhhh s ssss h
1h7w_2#2 ssssss hhhhhhhh hhhhh s ssss h
TARGET 799 ESGLQFLHSG ASVLQVCSAI QNQDFTVIED YCTGLKALLY LKSIEELADW
1h7w_2#2 800 esglqflhsg asvlqvcsav qnqdftviqd yctglkally lksieelqgw
TARGET hhhhhhhhh sss hhh hh hhhhh hhhhhhhhhh hh
1h7w_2#2 hhhhhhhhh sss hhh hh hhhhh hhhhhhhhhh hh
TARGET 849 DGQSPPIISH QKGKPVPRVA ELMGQKLPSF GPYLEQRKKI IAASKIRQKD
1h7w_2#2 850 dgqspgtesh qkgkpvpria elmgkklpnf gpyleqrkki iaeekmrlke
TARGET ss s sss hhhhhhhh hhhhhhhhh
1h7w_2#2 ss s sss hhhhhhhh hhhhhhhhh
TARGET 899 QNTACSPLQR KHFNSQKPIP AIKDVIGKSL QYLGTFGEMS IMEQVVALID
1h7w_2#2 900 qnaafppler kpfipkkpip aikdvigkal qylgtfgels nieqvvavid
TARGET hhh hh h sssssss
1h7w_2#2 hhh hh h sssssss
TARGET 949 EEMCINCGKC YMTCNDSGYQ AIQFDPETHL PTVSDTCTGC TLCLSVCPIM
1h7w_2#2 950 eemcincgkc ymtcndsgyq aiqfdpethl ptvtdtctgc tlclsvcpii
TARGET hh hhhhh sssss s ssss hhhhh
1h7w_2#2 hh hhhhhh sssss s ssss hhhhh
TARGET 999 DCIRMVSRAT PYQPKRGL - AGVLSRDAP DIESILALNP RVQAHATLRS
1h7w_2#2 1000 dcirmvsrtt pyepkrgl-- -apvlskdva diesilalnp rtqshaalhs
*
TARGET sssssss h hhhh
1h7w_2#2 sssssss h hhhh
TARGET 1046 TAAKKLDKKH WKRNTDKNCF TCEKLESNFD DIKHTTLGER GALREAVRCL
1h7w_2#2 31 tlakkldkkh wkrnpdkncf hceklennfd dikhttlger galreamrcl
TARGET hhhhhhhhh hh hhhhhhhh
1h7w_2#2 hhhhhhhhhh hh hhhhhhhh
TARGET 1096 KCADAPCQKS CPTSLDIKSF ITSIANKNYY GAAKLIFSDN PLGLTCGMVC
1h7w_2#2 81 kcadapcqks cpthldiksf itsisnknyy gaakmifsdn plgltcgmvc
TARGET hhhhh hhhh hhhhh hh hhhhhhhhh hhhhhh
1h7w_2#2 hhhhh hhhh hhhh hhh hhhhhhhhh hhhhhh
TARGET 1146 PTSDLCVGGC NLHAAEEGPI NIGGLQQFAT EVFKAMNIPQ IRNPSLPPPE
1h7w_2#2 131 ptsdlcvggc nlyateegsi nigglqqfas evfkamnipq irnpclpsqe
TARGET hh hhhhhhhhh hhhhh
1h7w_2#2 hh hhhhhhhhh hhhhh
TARGET 1196 HMPEAYSAKI ALFGAGPASI SCASFLARLG YSNITIFEKQ EYVGGLSTSE
1h7w_2#2 181 kmpeaysaki allgagpasi scasflarlg ysditifekq eyvgglstse
TARGET hh s ssss hhhh hhhhhhhhh ssssss hhhh
1h7w_2#2 hh s ssss hhhh hhhhhhhh ssssss hhhh
TARGET 1246 IPQFRLPYDV VNFEIELMKD LGVKIICGKS LSTDEMTLSS LKENGYRAAF
1h7w_2#2 231 ipqfrlpydv vnfeielmkd lgvkiicgks lseneitlnt lkeegykaaf
TARGET hh hhhhhhhhhh sssss hhh hhhh sss
1h7w_2#2 hh hhhhhhhhhh sssss s ss sss hhh hhhh sss
TARGET 1296 IGIGLPEPKK DHIFQGLTQV QGFYTSKDFL PLVAKSSKTG MCACHSPLPS
1h7w_2#2 281 igiglpepkt ddifqgltqd qgfytskdfl plvaksskag mcachsplps
TARGET ss sss ssssshhhh hhhhhhh
1h7w_2#2 ss sss ssssshhhh hhhhhhh
TARGET 1346 IRGAVIVLGA GDTAFDCATS ALRCGALRVF IVFRKGFVNI RAVPEEMELA
1h7w_2#2 331 irgavivlga gdtafdcats alrcgarrvf lvfrkgfvni ravpeevela
TARGET sssssssss hhhhhhhhh hhh sssss sss hhhhhhh
1h7w_2#2 sssssssss hhhhhhhhh hhh sssss sss hhhhhhh
TARGET 1396 KEEKCEFLPF LSPRKVIVKD GKIVAMQFVR TEQDETGNWV EDEEQTVRLK
1h7w_2#2 381 keekceflpf lsprkvivkg grivavqfvr teqdetgkwn ededqivhlk
TARGET h sssss sssssssss sssssssss ssss sss ss ssssss
1h7w_2#2 h sssss sssssssss sssssssss ssss sss ss ssssss
TARGET 1446 ADVVISAFGS VLEDPKVKEA LSPIKFNRWG LPEVNPETMQ TSEPWVFAGG
1h7w_2#2 431 advvisafgs vlrdpkvkea lspikfnrwd lpevdpetmq tsepwvfagg
TARGET s sssss ss s hhhhhh sss sss ss s sssss
1h7w_2#2 s sssss ss s hhhhhh sss sss ss s sssss
TARGET 1496 DVVGMANTTV ESVNDGKQAS WYIHKHIQAQ YGTSVPSQPT MPLFYTPVDL
1h7w_2#2 481 divgmanttv esvndgkqas wyihkyiqaq ygasvsakpe lplfytpvdl
TARGET hh hhhhhhhhhh hhhhhhhhhh hh
1h7w_2#2 hh hhhhhhhhhh hhhhhhhhhh hh
TARGET 1546 VDISVEMAGL RFPNPFGLAS ATPATSTPMI RRAFEAGWGF ALTKTFSLDK
1h7w_2#2 531 vdisvemagl kfinpfglas aapttsssmi rrafeagwgf altktfsldk
TARGET sss s ss sssss hhh hhhhhh ss sss
1h7w_2#2 sss s ss sssss hhh hhhhhh ss sss
TARGET 1596 DIVTNVSPRI IRGTTSGPLY GPGQSSFLNI ELISEKTAAY WCHSVTELKA
1h7w_2#2 581 divtnvspri vrgttsgpmy gpgqssflni elisektaay wcqsvtelka
TARGET ss sss ssssss hhh hhhhhhhhhh
1h7w_2#2 ss sss ssssss hhh hhhhhhhhhh
TARGET 1646 DFPDNILIAS IMCSYNKSDW MELSKMAEAS GADALELNLS CPHGMGERGM
1h7w_2#2 631 dfpdnivias imcsynkndw melsrkaeas gadalelnls cphgmgergm
TARGET h sssss s hhhh hhhhhhhhh sssss sss
1h7w_2#2 h sssss s hhhh hhhhhhhhh sssss sss
TARGET 1696 GLACGQDPEL VRNICRWVRQ AVRVPFFAKL TPNVTDIVSI ARAAKEGGAD
1h7w_2#2 681 glacgqdpel vrnicrwvrq avqipffakl tpnvtdivsi araakeggad
TARGET sss hhh hhhhhhhhhh h ssssss hhh hhhhhhh
1h7w_2#2 sss hhh hhhhhhhhhh h ssssss hhh hhhhhhh
TARGET 1746 GVTATNTVSG LMGLKADGTP WPAVGIGRRT TYGGVSGTAI RPIALRAVTA
1h7w_2#2 731 gvtatntvsg lmglkadgtp wpavgagkrt tyggvsgtai rpialravtt
TARGET ssss sss ssssss hhhhhhhhh
1h7w_2#2 ssss sss ssssss hhhhhhhhh
TARGET 1796 IARALPGFPI LATGGIDSAE SGLQFLHSGA SVLQVCSAIQ NQDFTVIEDY
1h7w_2#2 781 iaralpgfpi latggidsae sglqflhsga svlqvcsavq nqdftviqdy
TARGET hhhh ss sss hh hhhhhhhh sss hhhh h hhhhhh
1h7w_2#2 hhhh ss sss hh hhhhhhhh sss hhhh h hhhhhh
TARGET 1846 CTGLKALLYL KSIEELADWD GQSPPIISHQ KGKPVPRVAE LMGQKLPSFG
1h7w_2#2 831 ctglkallyl ksieelqgwd gqspgteshq kgkpvpriae lmgkklpnfg
TARGET hhhhhhhhhh h
1h7w_2#2 hhhhhhhhhh h
TARGET 1896 PYLEQRKKII AASKIRQKDQ NTACSPLQRK HFNSQKPIPA IKDVIGKSLQ
1h7w_2#2 881 pyleqrkkii aeekmrlkeq naafpplerk pfipkkpipa ikdvigkalq
TARGET hhhhhhhhh hhhhhhhhh hhh hhh
1h7w_2#2 hhhhhhhhh hhhhhhhhh hhh hhh
TARGET 1946 YLGTFGEMSI MEQVVALIDE EMCINCGKCY MTCNDSGYQA IQFDPETHLP
1h7w_2#2 931 ylgtfgelsn ieqvvavide emcincgkcy mtcndsgyqa iqfdpethlp
TARGET sssssss hhh hhhh s ssss ss
1h7w_2#2 sssssss hhh hhhhh s ssss ss
TARGET 1996 TVSDTCTGCT LCLSVCPIMD CIRMVSRATP YQPKRGLPL
1h7w_2#2 981 tvtdtctgct lclsvcpiid cirmvsrttp yepkrglpl-
TARGET sss hhhhh sssssss
1h7w_2#2 sss hhhhh sssssss
Template's ligands section
Ligands in the template:FAD : 2,FMN : 2,SF4 : 8.
Ligands in the template that will be assessed: FAD1188, FAD6, FMN1187, FMN5, SF41, SF41183, SF41184, SF41185, SF41186, SF42, SF43, SF44.
Model's ligands section
SF41
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.SF41 will be included in the model.
SF41: conservation:True, RMSD:True, included: True
SF42
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: 0.020
Given the properties calculated previously, the ligand z.SF42 will be included in the model.
SF42: conservation:True, RMSD:True, included: True
SF43
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.SF43 will be included in the model.
SF43: conservation:True, RMSD:True, included: True
SF44
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: 0.030
Given the properties calculated previously, the ligand z.SF44 will be included in the model.
SF44: conservation:True, RMSD:True, included: True
FMN5
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.FMN5 will be included in the model.
FMN5: conservation:True, RMSD:True, included: True
FAD6
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.FAD6 will be included in the model.
FAD6: conservation:True, RMSD:True, included: True
SF41183
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.SF41183 will be included in the model.
SF41183: conservation:True, RMSD:True, included: True
SF41184
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: 0.030
Given the properties calculated previously, the ligand z.SF41184 will be included in the model.
SF41184: conservation:True, RMSD:True, included: True
SF41185
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.SF41185 will be included in the model.
SF41185: conservation:True, RMSD:True, included: True
SF41186
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: 0.030
Given the properties calculated previously, the ligand z.SF41186 will be included in the model.
SF41186: conservation:True, RMSD:True, included: True
FMN1187
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.FMN1187 will be included in the model.
FMN1187: conservation:True, RMSD:True, included: True
FAD1188
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.FAD1188 will be included in the model.
FAD1188: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
1h7w 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: 1h7w.pdb2.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 0.734 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1h7wC
Model was succesfully built as DIMER.
Template Selection
- Start SMR-Pipeline for:8c3ca87b27615b4f38c3f7b4382309c7 on BC2-cluster at Fri Feb 22 20:55:01
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 1 go for
modeling ...
FATAL - No A3m 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 1h7wD (2-1019) 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:8c3ca87b27615b4f38c3f7b4382309c7 on BC2-cluster at Fri Feb 22 21:22:34
2013
Template Search
| Template Description |
|
||||||||||||||||||||
|
1h7w: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST |
|
||||||||||||||||||||
|
1gth: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND 5-IODOURACIL Solved by: X-RAY, Resolution: 2.25A, Identified by BLAST |
|
||||||||||||||||||||
|
1h7x: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX OF A MUTANT ENZYME (C671A), NADPH AND 5- FLUOROURACIL Solved by: X-RAY, Resolution: 2.01A, Identified by BLAST |
|
||||||||||||||||||||
|
1gte: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, BINARY COMPLEX WITH 5-IODOURACIL Solved by: X-RAY, Resolution: 1.65A, Identified by BLAST |
|
||||||||||||||||||||
|
1gt8: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND URACIL-4-ACETIC ACID Solved by: X-RAY, Resolution: 3.30A, Identified by BLAST |
|
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.