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" <d...@iwonka.med.virginia.edu>
Sent: Tuesday, April 05, 2011 5:00 PM
To: <CCP4BB@JISCMAIL.AC.UK>
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
