Is it possible to efile with attachments such as PDF? e.g., with a letter of explanation attached to Form 5329?

You cannot attach a PDF to an e-filed Form 1040 federal tax return in TurboTax. If IRS rules require an explanation for your Form 5329 , TurboTax will prompt you to enter the explanation and will include it in your e-filed tax return. Otherwise there is no need to attach an explanation. The IRS instructions for Form 1040 say "Do not attach correspondence or other items unless required to do so." If the IRS wants additional information, they will send you a letter asking for it.

@dlwright1 

TurboTax CD/download will let you enter an explanation for Form  1040 lines 4,5 and Form 5329, and then e-File.

I don't know about TurboTax Online.

The only PDF you can attach is your consolidated form 1099-B details (or equivalent) in PDF format.