The second descriptive output in section 3 is the secondary structure. In the PDB file 4NLL the secondary structure looks OK. Helices and strands have some length, and the percentages helix and strand seem OK. Obviously, unstructure proteins do exist, but their structure will (by definition!) not be solved...
10 20 30 40 50 60
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1 - 60 MKIVYWSGTGNTEKMAELIAKGIIESGKDVNTINVSDVNIDELLNEDILILGCSAMDDEV
( 1)-( 60) SSSSS TTTHHHHHHHHHHHHHHHTT SSSS333 HHHHTT TSSSSSS TTT
70 80 90 100 110 120
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61 - 120 LEESEFEPFIEEISTKISGKKVALFGSYGWGDGKWMRDFEERMNGYGCVVVETPLIVQNE
( 61)-( 120) TTTHHHHHHHH333 TT SSSSSSSSTTT THHHHHHHHHHHHTT SS T SSSSTT
130
|
121 - 138 PDEAEQDCIEFGKKIANI
( 121)-( 138) 333HHHHHHHHHHHHT
|
The PDB file 1PDX has as secondary structure:
10 20 30 40 50 60
| | | | | |
1 - 60 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKV
( 1)-( 60) SSSS TTT TT HHHHHHHHTTT T TTTT TTT SSS HHHHTTT
70 80 90 100
| | | |
61 - 106 PAANEREIGMLECVTAELKPNSRLCCQIIMTPELDGIVVDVPDRQW
( 61)-( 106) HHHHHHHHHT T TTSS 333 TTTTTSSSS T
|
and that warns me, because there seem to be many long, unstructured loops, and the few strands are very short. Indeed, if we look at the global structure scores we see:
1st generation packing quality : -1.793 2nd generation packing quality : -3.353 (poor) Ramachandran plot appearance : -7.372 (bad) chi-1/chi-2 rotamer normality : -7.488 (bad) Backbone conformation : -2.375 |
You find much more information about the DSSP software that determines the secondary structure from the coordinates at: the DSSP website.