| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1st6_Ai |
d1st6a2 | A183-A253,A652-A717 | All alpha proteins | Four-helical up-and-down bundle | alpha-catenin/vinculin | alpha-catenin/vinculin | Vinculin |
1jqn_Ac |
d1jqna_ | A256-A340,A341-A391 | Alpha and beta proteins (a/b) | TIM beta/alpha-barrel | Phosphoenolpyruvate/pyruvate domain | Phosphoenolpyruvate carboxylase | Phosphoenolpyruvate carboxylase |
Justification for analogy
The motif in 1st6: the 4-helix bundle uses corresponding parts in two duplicates. This is an interface motif. Each duplicate is also a 4-helix
bundle, but is mirror image to the interface motif. 1st6 is in the Four-helical up-and-down bundle fold in SCOP. So I cannot use
anything in this fold as analog to the hybrid motif, since it may bear homologous part to the interface motif. 1jqn is in "TIM
beta/alpha-barrel" fold.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 95 | 0.09474 | 2.78906 | 58.68421 | -13.32932 |
| dali | 100 | 0.07000 | 2.84146 | 60.25000 | -15.74259 |
| tm | 107 | 0.10280 | 3.33710 | 56.30841 | -13.78426 |
| fast | 90 | 0.08889 | 3.49934 | 48.88889 | -15.07207 |
In the alignments below, two upper-case letters are aligned, while two lower-case letters are NOT aligned. The two sequences in an alignment are NOT continuous in most cases (see their ranges). The superpositions are re-constructed from the corresponding alignments by minimizing the overall RMSD. In a PDB-format superposition file, the first domain is represented by chain S and the second domain is represented by chain A.
MANUAL alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1st6_Ai ------tHQEHRVMLVNSMNTVKELLPVLISAMKIFvttkn-------tksqgiEEALKNRNFTVEKMSAEINEIIRVLQLtsw-tankttvegiqatvKSARELTPQVVSAARILLRNpgNQAAYEHFETMKNQWIDNVekmtglvdeai 1jqn_Ac npnvtadITRHVLLLSRWKATDLFLKDIQVLVSELSmveatpellalvgeegaaEPYRYLMKNLRSRLMATQAWLEARLKGeelp-------kpeglltQNEELWEPLYACYQSLQACGm-GIIANGDLLDTLRRVKCFGvplv-------
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1st6_Ai --THQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTKS---------------QGIEEALKNRNFTVEKMSAEINEIIRvlqltswtankttvegiqatvksaRELTPQVVSAARILLRNP----GNQAAYEHFETMKNQWIDnvekmtglvdeai 1jqn_Ac npNVTADITRHVLLLSRWKATDLFLKDIQVLVSELSMVEAtpellalvgeegaaePYRYLMKNLRSRLMATQAWLEARLKG--------------eelpkpegllTQNEELWEPLYACYQSLQacgmGIIANGDLLDTLRRVKCF--------gvplv
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1st6_Ai ------THQEHRV-MLVNSMNTVKELLPVLISAMKIFVTTKNTKSQ---G----------IEEALKNRNFTVEKMSAEINEIIRVLQLTS-------WTANKTTVEGIQATVKSARELTPQVVSAARILLRNPGNQAAYEHFETMKNQWIDNV-EK-MTGLVDEAI 1jqn_Ac NPNVTA-DITRHVLLLSRWKATDLFLKDIQVLVSELS--M---VEATPELLALVGEEGAAEPYRYLMKNLRSRLMATQAWLEARLK-GEELPKPEGL--------------LTQNEELWEPLYACYQSLQACGMGIIANGDLLDTLRRVKCFGV-PL---V-----
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1st6_Ai T-------HQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTKS-------QGIEEAL--------KNRNFTVEKMSAEINEIIRVLQLTSWTANKTTVEGIQA----------------TVKSARELTPQVVSAARILLRNPGNQAA--YEHFE-TMKNQWIDNVEKMTGLVDEAI----- 1jqn_Ac -NPNVTADITRHVLLLSRWKATDLFLKDIQVLVSEL---------SMVEATPELLAL--VGEEGAAEPYRYLMKNLRSRLMATQAWLEA----------------RLKGEELPKPEGLLTQNEELWEPLYACYQSLQAC----------GMGIIANGDLLDTLRRVKCF---------GVPLV