d1nkta3d1ldja1

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1nkt_Ah	d1nkta3	A106-A123,A57-A96	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
1ldj_Ac	d1ldja1	A687-A724,A725-A776	All alpha proteins	DNA/RNA-binding 3-helical bundle	"Winged helix" DNA-binding domain	SCF ubiquitin ligase complex WHB domain	Anaphase promoting complex (APC)

Justification for analogy
In 1nkt, the 3-helix bundle uses one helix in the N-terminal extra all-alpha subdomain, one helix before the first strand in the Rossmann-like fold (this helix can be considered as part of the Rossmann fold), and one helix after the P-loop. This is a hybrid motif, but the topology is up-down-down. So we make a circular permutation.

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

1nkt_Ah   -----------------GKTLTCVLPAYLNALAGn---etlddLLPEAFAVAREAAWRvlDQRPFDVQVMGAAALHLG------------------
1ldj_Ac   pmkteqkqeqetthkniEEDRKLLIQAAIVRIMKmrkv----lKHQQLLGEVLTQLSS--RFKPRVPVIKKCIDILIEkeylervdgekdtysyla

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

1nkt_Ah   --------------------GKTLTC-VLPAYLNALAgnetlddLLPEAFAVAREAAWrvLDQRPFDVQVMGAAALHLG------------------
1ldj_Ac   pmkteqkqeqetthknieedRKLLIQaAIVRIMKMRK-----vlKHQQLLGEVLTQLS--SRFKPRVPVIKKCIDILIEkeylervdgekdtysyla

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

1nkt_Ah   --------------------GKTLTC-VLPAYLNALAGNETLDDLLP-EAFAVAREAAWRVLDQRPFDVQVMGAAA-LHLG------------------
1ldj_Ac   PMKTEQKQEQETTHKNIEEDRKLLIQAAI-VRIMKMR---KV--LKHQQLLGEVLTQLS-SR-FKPRVPVIKKCIDIL-IEKEYLERVDGEKDTYSYLA

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

1nkt_Ah   GKTLTCVLPAYLNALAGNET----------------LDDLLPEAFAVAREAAWRVLDQRPFDVQ-VMGAAALHLG-------------------------------------
1ldj_Ac   --------------------PMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKV-LKHQQLLGEVLTQLS-SRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA