| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1izn_Ai |
d1izna_ | A7-A42,B2-B33 | Multi-domain proteins (alpha and beta) | Subunits of heterodimeric actin filament capping protein Capz | Subunits of heterodimeric actin filament capping protein Capz | Capz alpha-1 subunit | Capz alpha-1 subunit |
2gsc_Ac |
d2gsca_ | A9-A63,A68-A125 |
Justification for analogy
In 1izn, the 4-helix bundle uses corresponding parts in the two chains. interface motif. Note that the two chains are not identical, but they are in the same superfamily in SCOP.
In 2gsc, the 4-helix bundle is an individual domain by itself.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 63 | 0.00000 | 2.73616 | 61.90476 | -3.46904 |
| dali | 67 | 0.04478 | 3.36420 | 52.23881 | -3.34110 |
| tm | 62 | 0.11290 | 2.49356 | 62.90323 | -6.01884 |
| fast | 62 | 0.03226 | 2.70466 | 62.09677 | -2.24301 |
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 1izn_Ai -----rvSDEEKVRIAAKFITHAPp-------gEFNEVFNDVRLLLNn----------------SDQQLDCALDLMRRL-----PPQQIEKNLSDLIDLVP------------ 2gsc_Ac rpherldAWRDSMELVEMIYRLTEvfpdqerygLTAQLRRAAVSIPSniaegaardysrflsiaRGSLSELDTQVQIAArlgysRSEDDQSVRRQVDLVFAkltalmnalrrr
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1izn_Ai -----RVSDEEKVRIAAKFITHA-------pPGEFNEVFNDVRLLLNN------------SDQQLDCALDLMRRL--------PPQQ-IEKNLSDLIDLVP------------ 2gsc_Ac rpherLDAWRDSMELVEMIYRLTevfpdqerYGLTAQLRRAAVSIPSNiaegaardysrfLSIARGSLSELDTQVqiaarlgySRSEdDQSVRRQVDLVFAkltalmnalrrr
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1izn_Ai ------R--VSDEEKVRIAAKFITHAPPGEFN-EVFNDVRLLL-NN-----------------------SDQQLDCALDLM-RRLPPQQIEKNLSDLI-DLVP---------------- 2gsc_Ac RPHERLDAWRDSMELVEMIYRLTEVFPDQERYGLTAQLRRA-AVSIPSNIAEGAARDYSRFLSIARGSLS-ELDTQVQIAARLGYS--RS-EDDQSVRRQ-VDLVFAKLTALMNALRRR
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1izn_Ai RVS--------DEEKVRIAAKFITH---APPGE----FNEVFNDVRLLLNN------------------SDQQLDCALDLMRR-----LPPQQIEKNLSDLIDLVP------------- 2gsc_Ac ---RPHERLDAWRDSMELVEMIYRLTEVFPDQERYGLTAQLRRAAVSIP--SNIAEGAARDYSRFLSIARGSLSELDTQVQIAARLGYSRSEDDQSVRRQVDLVF-AKLTALMNALRRR