AMBER Archive (2002)

Subject: Re: HIS residues

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Oct 24 2002 - 16:51:40 CDT

Hi,

If you look at the structure of histidine it can have three protonation
states:
- when N(eps) or N(delta) are protonated, you have the HID and HIE residue
types that are neutral
- when both N(eps) and N(delta) are protonated, you have the HIP residue
type and the total charge is +1

              peptide bond
                    |
                    NH O
                    | /
CH--------C---CH2---CH---C
| | \
N(eps) N(delta) peptide bond
 \ /
  \ /
    CH

So it depends on what you want to do with your structure, you have to
chose if you want to have a neutral or charged HIS or maybe you do not
want to protonate it at all...

Hope this is of some help,
Ioana

****************************************************************************
* Ioana Cozmuta * *
* NASA-AMES Research Center * "Gravitation can not be held responsible*
* Mail Stop 230-3 * for people falling in love" *
* Moffet Field * *
* phone: (650) 604-0993 * Albert Einstein*
****************************************************************************

On Thu, 24 Oct 2002, Joel Konkle-Parker wrote:

> I have a pdb of Acetylcholinesterase (1EEA) that has several HIS
> residues. From what I've read, I understand that LEAP doesn't use HIS,
> it changes it to one of HID, HIE, or HIP, by default HID, so it's best
> to change it within the pdb. Is this a critical item to check? If so,
> what's the best way to find out which type I have?
>
> -Joel
>
>