N-acetylgalactosamine lacking amide planarity restraint
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Hi, I'm refining a structure that includes an O-linked N-acetylgalactosamine (NGA) residue, and from the way it's behaving the N-acetyl amide clearly has no restraints on its planarity. It's currently twisted almost 45 degrees from planar despite having no close contacts. Cheers, Tristan
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Tristan
Can you send the model so I can check what is happening.
Cheers
Nigel
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Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Mon, Jan 18, 2016 at 5:19 AM, Tristan Croll
Hi,
I'm refining a structure that includes an O-linked N-acetylgalactosamine (NGA) residue, and from the way it's behaving the N-acetyl amide clearly has no restraints on its planarity. It's currently twisted almost 45 degrees from planar despite having no close contacts.
Cheers,
Tristan
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Hi Nigel,
Actually, this may have been due to a mistake on my part leading to a bad input structure. I will double-check tomorrow and let you know. I do know that many older structures containing N-acetyl sugars have the amide bond badly twisted suggesting that at some point the restraint libraries didn't cover it. If this case turns out to be my fault I apologise for the false alarm.
Best regards,
Tristan
________________________________
From: Nigel Moriarty
participants (2)
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Nigel Moriarty
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Tristan Croll