| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1gx3_Ah |
d1gx3a_ | A85-A185 | Alpha and beta proteins (a+b) | Cysteine proteinases | Cysteine proteinases | Arylamine N-acetyltransferase | Arylamine N-acetyltransferase |
1epa_Ac |
d1epaa_ | A3-A162 | All beta proteins | Lipocalins | Lipocalins | Retinol binding protein-like | Retinoic acid-binding protein |
Justification for analogy
The motif in 1gx3: compare d1gx3a_ with classic cysteine proteinase papain d1ppn__ (same superfamily), half of the barrel in 1gx3 is
absent in 1ppn. So this is a hybrid motif and is analog to true barrels in all-beta class. Note that the cysteine proteinase superfamily is
very diverged in structures.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 77 | 0.05195 | 4.42275 | 46.10390 | -18.48876 |
| dali | 79 | 0.05063 | 3.35734 | 54.74684 | -18.29170 |
| tm | 87 | 0.08046 | 3.50605 | 52.58621 | -19.27938 |
| fast | 70 | 0.04286 | 3.19307 | 56.78571 | -16.24640 |
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 1gx3_Ah --------gfEVERL-SGRVVwmraddaplpaQTHNVLSVAVPGa--dGRYLVDVgfggqtltSPIRLEA-------GPVQQTRHEPYRLTRHG------DDHTLAAQVRGEWQPlYTFTTEPRP----------------------------------------- 1epa_Ac vkdfdiskflGFWYEiAFASKmgtp--glahkEEKMGAMVVELKenllALTTTYYse---dhcVLEKVTAtegdgpaKFQVTRLSGKKEVVVEAtdyltyAIIDITSLVAGAVHR-TMKLYSRSLddngealynfrkitsdhgfsetdlyilkhdltcvkvlqsaa
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1gx3_Ah ------gfeVERLSG-RVVWMraddaplpaq--THNVLSVAVpgADGRYLVDvGFGG--qtltSPIR-----leAGPVQQTRHEPYRLTRHG------DDHTLAAQVRGEWQPLYTFTTEPRP---------------------------------------- 1epa_Ac vkdfdiskfLGFWYEiAFASKmgtpglahkeekMGAMVVELK--ENLLALTT-TYYSedhcvlEKVTategdgpAKFQVTRLSGKKEVVVEAtdyltyAIIDITSLVAGAVHRTMKLYSRSLDdngealynfrkitsdhgfsetdlyilkhdltcvkvlqsaa
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1gx3_Ah ---------GFEVERLSGRVVWMR----------ADDAPLPAQTHNVLSVAVPGADGRYLVDVGFGG---QTLTSPIRLE----AGPVQQTRHEPYRLTRHGD------DHTLAAQVRGEWQPLYTFTTEPRP----------------------------------------- 1epa_Ac VKDFDISKF--LGFWYEIAFASKMGTPGLAHKEE---------KMGAMVVEL-KENLLALTTTYYSEDHC-VLEKVTATEGDGPAKFQVTRLSGKKEVVVEATDYLTYAIIDITSLVAGAVHRTMKLY-SRSLDDNGEALYNFRKITSDHGFSETDLYILKHDLTCVKVLQSAA
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1gx3_Ah GFEV----------ERLSG-RVVWMRADDAPLPAQT--------------HNVLSVAVPGADGRYLVDVGFGGQTLT---------SPIRLEA-----GPVQQTRHEPYRLTRHGD-------DHTLAAQVRGEWQPL-YTFTTEPRP------------------------------------------- 1epa_Ac ----VKDFDISKFLGFWYEIAFAS------------KMGTPGLAHKEEKMGAMVVELKE--NLLALTTT--------YYSEDHCVLEKVTATEGDGPAKFQVTRLSGKKEVVVEA-TDYLTYAIIDITSLVAGAVHRTMKLYSR----SLDDNGEALYNFRKITSDHGFSETDLYILKHDLTCVKVLQSAA