Hi Heping,
Thanks for the list. It is very helpful and interesting. Out of curiosity:
how did you generate this list? Is there a way to search none-linear motifs
in PDB? Or did you write a script for searching database?
BTW, the ALA in 1xm7 looks unreal. A three-way tri-sulfide? The electron
density for the C155 seems too weak to support the C155-C157 linkage. Guess
this one should not be counted.
Zhijie
--------------------------------------------------
From: "Heping Zheng" <[log in to unmask]>
Sent: Tuesday, April 05, 2011 5:00 PM
To: <[log in to unmask]>
Subject: Re: [ccp4bb] disulfide bond question
> Ronnie --
>
> The list that I have in a home database contains 89 instances of a CXC in
> 53 files when C-C forms a disulfide bond. The records returned are ordered
> by the name of "X" residue from CXC motif for convenience.
>
> There is indeed PRO in one case (2zxt), but it is not the major
> observation in CXC motif.
>
> hope this helps
>
> cheers
>
> -- heping
>
>
> pdbid | resn-X | chainids | resseq
> -------+---------+------------------------+--------
> 1xm7 | ALA | A, B | 156
> 1zp0 | ALA | B | 162
> 2blf | ALA | A | 244
> 2bpb | ALA | A | 244
> 2c9x | ALA | A | 244
> 2ca3 | ALA | A | 244
> 2ca4 | ALA | A | 244
> 2b5g | ARG | B, A | 121
> 3bj8 | ARG | B, A | 121
> 2bcf | ASN | A | 101
> 1dbi | ASP | A | 138
> 1wrj | ASP | A | 30
> 3inj | CYS | E | 302
> 1ssu | GLN | A | 20
> 3me2 | GLU | R | 126
> 3me4 | GLU | A, B | 126
> 3nzy | GLU | B, D | 126
> 1jr8 | GLY | B, A | 110
> 1jra | GLY | B, D, C, A | 110
> 2bxr | GLY | B, A | 322
> 3i8i | GLY | 4 | 17
> 3i9c | GLY | 4 | 17
> 3lvt | GLY | A | 355
> 2he8 | HIS | A, B | 6
> 2ipg | HIS | B, A | 6
> 2p5n | HIS | A, B | 6
> 3cv6 | HIS | A, B | 6
> 3fac | HIS | B | 6
> 3fjn | HIS | A, B | 6
> 1z3s | ILE | B, A | 434
> 1z3u | ILE | A, B, C, D | 434
> 2gy7 | ILE | A | 434
> 2irm | LEU | A | 52
> 1cx8 | PHE | G, B, F, H, D, C, A, E | 557
> 1de4 | PHE | F, C, I | 557
> 1ewk | PHE | A, B | 290
> 1ewt | PHE | B, A | 290
> 1ewv | PHE | B, A | 290
> 1isr | PHE | A | 290
> 1iss | PHE | B, A | 290
> 1suv | PHE | B, A | 557
> 1t3n | PHE | B | 830
> 2nsu | PHE | A, B | 557
> 3lmk | PHE | A, B | 277
> 2zxt | PRO | A | 397
> 1mec | SER | 3 | 87
> 1nhr | SER | A | 41
> 1tmf | SER | 3 | 88
> 2mev | SER | 3 | 87
> 3dxu | SER | A | 311
> 2a4h | THR | A | 81
> 2ozk | VAL | C, A | 291
> 2w8n | VAL | A | 341
> (53 rows)
>
>
>
>
> On 05/04/2011 13:55, Ronnie wrote:
>> I have a question related to protein structure, but not crystallography
>> per se. Has anyone see a disulfide forming between the two cys of "CXC"
>> in the middle of a loop, and create a sharp turn, where X is not a
>> proline? I seems to me that geometrically this would be possible but I
>> am not sure how stable it is, or how energetically unfavorable it might
>> be.
>>
>> thanks so much for your input!
>>
>> Ronnie
|