SWISS-MODEL Repository 
Uniprot features:
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 ] |
Alignment
TARGET 1 MGVPAF FRWLSRKYPS VIIECNENKQ VDADTGRNIY EDPTLPNPNG
3fqdA 0 as--xgvpal frllsrkfak vitpvieapt eklpdgteie pdlslpnpng
TARGET hhh hhhhhhh sssss sss sss
3fqdA hhh hhhhhhh sssss sss sss
TARGET 47 IEFDNLYLDM NGIIHPCTHP EDKPAPKNED EMMVAIFECI DRLFGIVRPR
3fqdA 47 vecdnlyldx ngivhpcshp edrpapeted exxvavfeyt drilaxvrpr
TARGET sssssss hhhhhhh hh hhhhhhhhhh hhhhhhh
3fqdA sssssss hhhh hh hhhhhhhhhh hhhhhhh
TARGET 97 KLLYMAIDGV APRAKMNQQR SRRFRAAKET TEKRLEIARI REELLSRGCK
3fqdA 97 qllfiaidgv aprakxnqqr srrfrssrea alkeeelqaf ieeakqqgip
TARGET sssssss hhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhh
3fqdA sssssss hhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhh s
TARGET 147 LPPEKEKGEH FDSNCITPGT PFMDRLSKCL HYFVHDRQNN NPAWKGIKVI
3fqdA 147 idenatkkks wdsncitpgt pfxdtlaksl ryyiinklns dpcwrnvrfi
TARGET hhhh hhhhhhhhh hhhhhhhh sss
3fqdA sshhhh hhhhhhhhh hhhhhhhh sss
TARGET 197 LSDANVPGEG EHKIMDYIRK QRAQPDHDPN TQHVLCGADA DLIMLGLATH
3fqdA 197 lsdasvpgeg ehkixefirs qrvkpeydpn thhvvyglda dlixlglath
TARGET ss h hhhhhhhhhh hh sssss hhhhhhhh
3fqdA ss h hhhhhhhhhh hh sssss hhhhhhhh
TARGET 247 EPNFTIIREE FLPNKPRPCD ICNGFGHEMD KCVGLGATAP TSANFKPDVP
3fqdA 247 ephfrvlred vfkeerl--- ---gikrldd k--------- ----------
TARGET ssssss hhhh hh hhh hhhhhhhhh hhhhhhhh
3fqdA ssssssss hhh sss
TARGET 297 IGAEVKFIFV RLSVLREYLK QTLEMPNLPF EYSFERALDD WVFMCFFVGN
3fqdA 291 -----pfiwl nvsilreyle velyvpnlpf pfdleraidd wvffiffvgn
TARGET hh ssss sshhhhhhhh hhh hhhhhhh hhhhhhh
3fqdA sssss sshhhhhhhh hhh hhhhhhh hhhhhhh
TARGET 347 DFLPHLPSLE IREGAVDRLV ELYKKCVYKT RGYLTDSGDV NLDRVQLIMT
3fqdA 336 dflphlpsld irdgaverlt eiwraslphx ggyltldgsv nlaraevils
TARGET hhhhhh hhhhhhh hhhhhhhhh
3fqdA hhhhhh hhhhhhhhh hhhhhhhhh
TARGET 397 DLGNAEDQIF KSRQRREEQ ---------- ---------- ----------
3fqdA 386 avgnqeddif krlkqqedrr ndtvrlyepg yreryyeqkf hispdepeki
TARGET hhhhhhhhhh hhhhhhh
3fqdA hhhhhhhhhh hhhhhhh hhhhhhhh hhh
TARGET ---------- ---------- ---------- ---------- ----------
3fqdA 611 reavkhyvhg lcwvllyyyq gcpswtwyyp yhyapfaadf kdlasidvkf
TARGET
3fqdA hhhhhhhhhh hhhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
3fqdA 661 elnqpfkpye qllgvlpaas knnlpeklqt lxtdenseii dfypenftid
TARGET
3fqdA hhh hhhh hhhhh h sss
TARGET ---------- ---------- ---------- ---------- ----------
3fqdA 711 lngkkfewqg vallpfiden rllnavskiy pqlteeeskr nedgstllfi
TARGET
3fqdA sss hh hhhhhhhhhh h hhhhhh sssss
TARGET ---------- ---------- ---------- ---------- ----------
3fqdA 761 sehhpxfsel vkqlyskkrq gkplklsgkx ahglfgkvnt ndsvipnvsv
TARGET
3fqdA ss hhhhh hhhh sss ssss
TARGET ---------- ---------- ---------- ---------- ----------
3fqdA 811 qcpidvtsad alqkygsidd nqsislvfev pkshfvhksx llrgvkxpnr
TARGET
3fqdA hh hhhh ssssssss
TARGET ---------- ----
3fqdA 861 vltpedinqv raer
TARGET
3fqdA hhhhhhh hhh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3fqd is annotated as HETERO 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: 3fqd.pdb1.gz
Quaternary Structure Modelling of the Target Protein
3fqd_1
Template Selection
- Start SMR-Pipeline for:b8f92b686080314929298d254b0b2566 on BC2-cluster at Tue May 7 07:53:16
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- No A3m found
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modified template library
- Summarize templates:
- No template with A found
- No template with B found
- No template with C 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:4): model based on new templates
- Send 4 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *************************************
- building model based on 3fqdA (1-415) was successful
- *****************
- building model based on 2y35A (476-664) was successful
- *************************
- building model based on 3fqdA (479-761) was successful
- ********************************************************************
- building model based on 3fqdA (1-768) 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:b8f92b686080314929298d254b0b2566 on BC2-cluster at Tue May 7 08:16:29
2013
Template Search
| Template Description |
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3fqd: CRYSTAL STRUCTURE OF THE S. POMBE RAT1-RAI1 COMPLEX Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH |
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2y35: CRYSTAL STRUCTURE OF XRN1-SUBSTRATE COMPLEX Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH |
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3q8l: CRYSTAL STRUCTURE OF HUMAN FLAP ENDONUCLEASE FEN1 (WT) IN SUBSTRATE 5'-FLAP DNA, SM3+, AND K+ Solved by: X-RAY, Resolution: 2.32A, Identified by HHSEARCH |
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3ory: CRYSTAL STRUCTURE OF FLAP ENDONUCLEASE 1 FROM HYPERTHERMOPARCHAEON DESULFUROCOCCUS AMYLOLYTICUS Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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3q8k: CRYSTAL STRUCTURE OF HUMAN FLAP ENDONUCLEASE FEN1 (WT) IN PRODUCT 5'-FLAP DNA, SM3+, AND K+ Solved by: X-RAY, Resolution: 2.32A, Identified by HHSEARCH |
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3qeb: CRYSTAL STRUCTURE OF HUMAN EXONUCLEASE 1 EXO1 (WT) IN COMPAND MN2+ (COMPLEX III) Solved by: X-RAY, Resolution: 3.10A, Identified by HHSEARCH |
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3qe9: CRYSTAL STRUCTURE OF HUMAN EXONUCLEASE 1 EXO1 (D173A) IN CDNA (COMPLEX I) Solved by: X-RAY, Resolution: 2.51A, Identified by HHSEARCH |
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3qea: CRYSTAL STRUCTURE OF HUMAN EXONUCLEASE 1 EXO1 (WT) IN COMP(COMPLEX II) Solved by: X-RAY, Resolution: 3.10A, Identified by HHSEARCH |
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1a77: FLAP ENDONUCLEASE-1 FROM METHANOCOCCUS JANNASCHII Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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1a76: FLAP ENDONUCLEASE-1 FROM METHANOCOCCUS JANNASCHII Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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3q8m: CRYSTAL STRUCTURE OF HUMAN FLAP ENDONUCLEASE FEN1 (D181A) WITH SUBSTRATE 5'-FLAP DNA AND K+ Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH |
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1rxw: CRYSTAL STRUCTURE OF A. FULGIDUS FEN-1 BOUND TO DNA Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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1ul1: CRYSTAL STRUCTURE OF THE HUMAN FEN1-PCNA COMPLEX Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH |
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1rxv: CRYSTAL STRUCTURE OF A. FULGIDUS FEN-1 BOUND TO DNA Solved by: X-RAY, Resolution: 2.50A, 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.