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
3ufbA 12 adqpmttaqq lgaivkssrq imrkdkglng dldrlpmltw imflkflddl
3ufbA hhh hhhhhhhhhh hhh hhhhhhhhhh hhhhhhhhhh
3ufbA 62 eqmreteavl egksfqpaie apyrwrdwaa ieggitgdel iafinndeam
3ufbA hhhhhhhhhh h hhhh hhh hhhhh ssss
3ufbA 112 rpdgtrgigl faylrslqgd nggdrrdvia tvfkgmqnrm ingyllrdvv
3ufbA s sssssh hhhhhh hhhhh hhhh hhhhhhhh
TARGET 1 KGTT SFEAELSLVS
3ufbA 162 dkingihfns seemhtlsrl yetmlremrd aagd--sgef ytprpvvrfm
TARGET hhhhhhh
3ufbA hhhh hhhhhhhhhh hhhhhhhhh hhhhhhh
TARGET 15 ANIAQVKPGT IMYDPFAGTG SFLVAGGHFG ---------- -----SLVIG
3ufbA 210 vevmdpqlge svldpacgtg gflveafehl erqcktvedr evlqessifg
TARGET hhhh ssss hhhhhh sss
3ufbA hhhh ssss hhhhhhhhhh hh hhhh hhhh ssss
TARGET 50 SDIDGRMIRG KGAQVNISAN FKKYGESSQF LDVLTMDFTN NALRNNL---
3ufbA 260 geakslpyll v------qmn lllhgleyp- -ridpenslr fplremgdkd
TARGET ss hhhhh h hhhh sss sss
3ufbA ss hhhhhh h hhh hhhh sss
TARGET 97 VIDTILCDPP YGIRESIKVL GAKDPERFLG KEDMEIDGEK AYLRRDYIPT
3ufbA 302 rvdviltnpp fggeeekgil ---------- -gnf------ ---pedmqta
TARGET sssss sss hh hhhhhhhh hh ss s s
3ufbA sssss sss hhh h s
TARGET 147 KKPYALDSLL DDLLQYSSER LPIGGRLAFW MPT--ANDAN IE----TIVP
3ufbA 332 etamlflqli mrklkrpghg sdnggraavv vpngtlfsdg isarikeell
TARGET sshhhhhhhh hh ssssss s
3ufbA sshhhhhhhh hh ssssss s hhhh hhhhhhhhh
TARGET 191 MHENLELKYN CVQE-F---N KWSRRLLVYI NRG ------ ----------
3ufbA 382 knfnlhtivr lpegvfapyt diagnllffd rsgptddiwy yqitvpegrk
TARGET sssssss s sssssss s
3ufbA h sssssss s sssssss s sssss sss
TARGET ---------- ---------- ---------- ---------- ----------
3ufbA 432 kytktkpmes hefdeclnww snrivnqnaw kesaseiiky sesgqlidvn
TARGET
3ufbA h hhhhhh sss sssshhh ss s sss
TARGET ---------- ----
3ufbA 482 ldrknpnsle vleh
TARGET
3ufbA h hh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3ufb 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: 3ufb.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 0.002 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Tue Feb 19 00:26:07
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 C found
- No template with A found
- No template with B found
- No template with D found
- No template with A found
- No template with B found
- No template with C 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:1): model based on new templates
- Send 1 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ****************************************
- building model based on 3ufbA (188-406) 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:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Tue Feb 19 00:28:02
2013
Template Search
| Template Description |
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4hc4: HUMAN HMT1 HNRNP METHYLTRANSFERASE-LIKE PROTEIN 6 (S. CERE Solved by: X-RAY, Resolution: 1.97A, Identified by HHSEARCH |
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3ufb: CRYSTAL STRUCTURE OF A MODIFICATION SUBUNIT OF A PUTATIVE RESTRICTION ENZYME FROM VIBRIO VULNIFICUS YJ016 Solved by: X-RAY, Resolution: 1.80A, Identified by HHSEARCH |
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2igt: CRYSTAL STRUCTURE OF THE SAM DEPENDENT METHYLTRANSFERASE FROM AGROBACTERIUM TUMEFACIENS Solved by: X-RAY, Resolution: 1.89A, Identified by HHSEARCH |
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4htf: CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE-DEPENDENT METHYLFROM ESCHERICHIA COLI IN COMPLEX WITH S-ADENOSYLMETHIONIN Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH |
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3hm2: CRYSTAL STRUCTURE OF PUTATIVE PRECORRIN-6Y C5,15- METHYLTRANSFERASE TARGETED DOMAIN FROM CORYNEBACTERIUM DIPHTHERIAE Solved by: X-RAY, Resolution: 2.21A, Identified by HHSEARCH |
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3ou7: DHPI-SAM-HEP COMPLEX Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH |
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3ou2: DHPI-SAH COMPLEX STRUCTURE Solved by: X-RAY, Resolution: 1.50A, Identified by HHSEARCH |
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4hg2: THE STRUCTURE OF A PUTATIVE TYPE II METHYLTRANSFERASE FROMANAEROMYXOBACTER DEHALOGENANS. Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH |
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3ou6: DHPI-SAM COMPLEX Solved by: X-RAY, Resolution: 2.30A, 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.