| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1tv8_Ah |
d1tv8a_ | A160-A259 | Alpha and beta proteins (a/b) | TIM beta/alpha-barrel | Radical SAM enzymes | MoCo biosynthesis proteins | Molybdenum cofactor biosynthesis protein A MoaA |
1t3e_Ac |
d1t3ea3 | A499-A653 | Alpha and beta proteins (a/b) | Molybdenum cofactor biosynthesis proteins | Molybdenum cofactor biosynthesis proteins | MoeA central domain-like | Gephyrin, domain 5 |
Justification for analogy
The motif in 1tv8: a hybrid motif in an opened TIM-barrel.
1t3e is basically Rossmann-like.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 72 | 0.08333 | 2.94504 | 61.80556 | -17.22593 |
| dali | 81 | 0.08642 | 4.14713 | 54.01235 | -19.62587 |
| tm | 78 | 0.10256 | 3.22154 | 59.29487 | -19.08024 |
| fast | 67 | 0.07463 | 3.24071 | 54.10448 | -13.77633 |
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 1tv8_Ah lNVKVNVVIQKg---------------------------------------iNDDQIIPMLEYFKDKHIEIRFIEFMdvgndngwdfskvvtkDEMLTMIEQHFEIDPVEpkyf---geVAKYYRHKD--NGVQFGLITSVsqs----------------------- 1t3e_Ac -PVVAVMSTGNellnpeddllpgkirdsnrstllatiqehgyptinlgivgdNPDDLLNALNEGISRADVIITSGGV----------------DYLKQVLDIDLHAQIHFgrvfmkpglPTTFATLDIdgVRKIIFALPGNpvsavvtcnlfvvpalrkmqgildpr
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1tv8_Ah lNVKVNVVIQKGI-------------------------------------NDDQ--IIPMLEYFKDKHIEIRFIEfmdvgndngwdfskvvtKDEMLTMIEQHFEIDPVEpKYFG---EVAKYYRHKD--NGVQFGLITSVSQS----------------------- 1t3e_Ac -PVVAVMSTGNELlnpeddllpgkirdsnrstllatiqehgyptinlgivGDNPddLLNALNEGISRADVIITSG----------------gVDYLKQVLDIDLHAQIHFgRVFMkpgLPTTFATLDIdgVRKIIFALPGNPVSavvtcnlfvvpalrkmqgildpr
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1tv8_Ah LNVKVNVVIQK-------------------------------------GIN-D-DQIIPMLEYFKDKHIEIRFIEFMDVGNDNGWDFSKVVTKDEMLTMIEQHFEIDPVE---PKYFG-EV--AKYYRHKD--NGVQFGLITSV--SQS----------------------- 1t3e_Ac PVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGI-VGDNPDDLLNALNEGISRADVIITSGG---------------V-DYLKQVLDIDLHAQIHFGRV---FMKPGLPTTFATLDIDGVRKIIFALPGNPV--SAVVTCNLFVVPALRKMQGILDPR
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1tv8_Ah LN-VKVNVVIQKGIN-------------------------------------------DDQIIPMLEYFKDKHI--EIRFIEFMDVGNDNGWDFSKVVT--KDEMLTMIEQHFEIDPVE-PKYFGE---VAKYYRHKD---NGVQFGLITSVSQS---------------------------- 1t3e_Ac --PVVAVMSTG----NELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISR--ADVIITS------------------GGVDYLKQVLDIDLHAQIHFGRVFMK-PGLPTTFATLD-IDGVRKIIFALP-----GNPVSAVVTCNLFVVPALRKMQGILDPR