| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1l6r_Ah |
d1l6ra_ | A36-A82,A148-A164 | Alpha and beta proteins (a/b) | HAD-like | HAD-like | Predicted hydrolases Cof | Phosphoglycolate phosphatase, PGPase |
1nrv_Ac |
d1nrva_ | A429-A502,A503-A533 | Alpha and beta proteins (a+b) | SH2-like | SH2 domain | SH2 domain | Growth factor receptor-bound protein 10, GRB10 |
Justification for analogy
The motif in 1l6r: two strands are insertions; hybrid motif in a Rossmann structure.
The motif in 1nrv: core motif in SH2 fold.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 51 | 0.03922 | 2.26572 | 63.72549 | -31.28880 |
| dali | 56 | 0.03571 | 2.72612 | 61.60714 | -28.94716 |
| tm | 58 | 0.03448 | 3.14885 | 62.06897 | -28.02880 |
| fast | 43 | 0.02326 | 2.24971 | 64.53488 | -29.21801 |
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 1l6r_Ah --ltvsLLSG-NVIPVVYALKIFLGIn--GPVFGEn-----gGIMFDN---DGSIKKFFs-------------geDKAFAVNKLKEMysl---------- 1nrv_Ac ihrtqhWFHGrISREESHRIIKQQGLvdgLFLLRDsqsnpkaFVLTLChhqKIKNFQILpctffslddgntkfsdLIQLVDFYQLNKgvlpcklkhhcir
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1l6r_Ah --ltvsLLSG-NVIPVVYALKIFLGIN--GPVFGE-----ngGIMFDND---GSIKKFFS-------------GEDKAFAVNKLKEMY----------sl 1nrv_Ac ihrtqhWFHGrISREESHRIIKQQGLVdgLFLLRDsqsnpkaFVLTLCHhqkIKNFQILPctffslddgntkfSDLIQLVDFYQLNKGvlpcklkhhcir
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1l6r_Ah -----LTVSLLSG-NVIPVVYALKIFLGIN--GPVFGEN-----GGIMFDND---GSIKKFFS-G-E----------DKAFAVNKLKEMYSL-------------- 1nrv_Ac IHRTQ---HWFHGRISREESHRIIKQQGLVDGLFLLRDSQSNPKAFVLTLCHHQKIKNFQILPCTFFSLDDGNTKFS--DL-IQLVDFYQLNKGVLPCKLKHHCIR
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1l6r_Ah LTVSLLSG-----------NVIPVVYALKIFLGING--PVFGENGG---------IMFDND----GSIKKFFSGED-----------------KAFAVNKLKEMYSL-------------- 1nrv_Ac --------IHRTQHWFHGRISREESHRIIKQQGLVDGLFLLR----DSQSNPKAFVLTLC-HHQKIKNFQIL----PCTFFSLDDGNTKFSDLIQLVDFYQLN----KGVLPCKLKHHCIR