d1lwda_d1a5t_1

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1lwd_Ah	d1lwda_	A17-A36,A328-A373,A393-A413	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	NADP-dependent isocitrate dehydrogenase
1a5t__c	d1a5t_1	208-237,238-305,306-329	All alpha proteins	DNA polymerase III clamp loader subunits, C-terminal domain	DNA polymerase III clamp loader subunits, C-terminal domain	DNA polymerase III clamp loader subunits, C-terminal domain	delta prime subunit

Justification for analogy
The motif in 1lwd: the 4-helix bundle uses the first and the last helices in the core structure, the other two helices come from C-terminal extension. So this is a hybrid motif, but the topology is down-down-up-down.

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

1lwd_Ah   --DEMTRIIWQFIKEKlILPHv--------------NPIASIFAWTRGLEHRgkldg--------------nqdLIRFAQTLEKVCVETVESGamt--LNTSDFLDTIKSNLDRALGrq---
1a5t__c   dnWQARETLCQALAYS-VPSGdwysllaalnheqapARLHWLATLLMDALKR-----vtnvdvpglvaelanhlSPSRLQAILGDVCHIREQLmsvtgINRELLITDLLLRIEHYLQpgvvl

DALI alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1lwd_Ah   --DEMTRIIWQFIKEKlILPH--------------vNPIASIFAWTRGLEHR---------gkldgnqDLIRFAQTLEKVCVETVESG--amtlNTSDFLDTIKSNLDRALGRQ---
1a5t__c   dnWQARETLCQALAYS-VPSGdwysllaalnheqapARLHWLATLLMDALKRvtnvdvpglvaelanhLSPSRLQAILGDVCHIREQLmsvtgiNRELLITDLLLRIEHYLQPGvvl

TM alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1lwd_Ah   DE-MTRIIWQFIKEKLI-LPHV--------------NPIASIFAWTRGLEHRGKL----------D--GN-QDLIRFAQTLEKVC-VET-VE--SGAMTLNTSDFLDTIKSNLDRAL-G--RQ-
1a5t__c   DNW-QA-RETLCQA--LAYSVPSGDWYSLLAALNHEQAPARLHWLATLLMDALKRVTNVDVPGLVAELANHLS-PSRLQAILGDVCHIREQLMS-VTGINRE-LLITDLLLRIEH-YLQPGVVL

FAST alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1lwd_Ah   D---EMTRIIWQFIKEKLILPHVN-----------------PIASIFAWTRGLEHRGKLDGN-------------------QDLIRFAQTLEKVCVETVESGAMTLN-----TSDFLDTIKSNLDRALGRQ-----
1a5t__c   -DNWQARETLCQALAYS-------VPSGDWYSLLAALNHEQAPARLHWLATLLMDALKR---VTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMS-------VTGINRELLITDLLLRIEHYLQ--PGVVL