| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1axn__i |
d1axn__ | 77-110,269-284 | All alpha proteins | Annexin | Annexin | Annexin | Annexin III |
1nkt_Ah |
d1nkta3 | A1-A56,A57-A82 | Alpha and beta proteins (a/b) | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | Tandem AAA-ATPase domain | Translocation ATPase SecA, nucleotide-binding domains |
Justification for analogy
The motif in 1axn: the 3-helix bundle uses helix 5 in the 1st duplicate, helix 1 in the 2nd duplicate, and helix 2 in the 5th duplicate.
This is an interface motif at the interface of three duplicates and in any one duplicate, the arrangement of helix
1,2,5 is different than the arrangement in the interface motif.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 44 | 0.06818 | 2.62732 | 64.77273 | -22.40007 |
| dali | 48 | 0.06250 | 3.03673 | 59.89583 | -22.48441 |
| tm | 46 | 0.04348 | 2.44408 | 70.10870 | -23.57557 |
| fast | 45 | 0.02222 | 3.09623 | 55.00000 | -24.57184 |
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 1axn__i --------------------lSGHFEHLMVALVTPPAVFDAKQLKKSMKgagtn--------DEFTLNRIMVSRSEID---- 1nkt_Ah ilskllrlgegrmvkrlkkvaDYVGTLSDDVEKLTDAELRAKTDEFKRRladqknpetlddlLPEAFAVAREAAWRVLdqrp
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1axn__i --------------------lSGHFEHLMVALVTPPAVFDAKQLKKSMK----gAGTN----DEFTLNRIMVSRSEID---- 1nkt_Ah ilskllrlgegrmvkrlkkvaDYVGTLSDDVEKLTDAELRAKTDEFKRRladqkNPETlddlLPEAFAVAREAAWRVLdqrp
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1axn__i ----------------------LSGH-FEHLMVALVTPPAVFDAKQ-LKKSMK--GA--GT-N---DEFTLNRIMVSRSEID---- 1nkt_Ah ILSKLLRLGEGRMVKRLKKVAD--YVGT-LSDDVEKLTDAELRA-KTDEFKRRLADQKNPETLDDLLPEAFAVAREAAWRVLDQRP
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1axn__i LS----------------------GHFEHLMVALVTPPAV---FDAKQLKKSMKGAGTN-------DEFTLNRIMVSRSEID----- 1nkt_Ah --ILSKLLRLGEGRMVKRLKKVADYVGTLSDDVEKLTDAELRAKTDEFKRRLADQKN--PETLDDLLPEAFAVAREAAWRV-LDQRP