[BiO BB] How to download Protein complexes from PDB ?

Shameer Khadar skhadar at gmail.com
Thu Sep 13 07:38:37 EDT 2007

Dear Mike,
Thanks for your reply.

> I'm not entirely sure what you mean but I do know I've had to guess a lot
> with the ncbi structure database. To test my molecule viewer, I had to
> write
> several new scripts like this:
> 142  pdbget -out xxx -structure "gaba complex"
> 143  cat xxx
> 144  pdbget -get 29354 1sff.pdb
> I've got another script that the above calls:
> $ eutilsnew -v -out asdf -structure  -report docsum  -retmode text
> cytochrome
> $ more asdf
> 1: 2HL7
> Crystal Structure Of The Periplasmic Domain Of Ccmh From Pseudomonas
> Aeruginosa
> [mmdbId:47389]
> 2: 2Z3U
> Crystal Structure Of Chromopyrrolic Acid Bound Cytochrome P450 Stap
> (Cyp245a1)
> [mmdbId:47341]
> 3: 2Z3T
> Crystal Structure Of Substrate Free Cytochrome P450 Stap (Cyp245a1)
> [mmdbId:47340]
> 4: 2V0M
> Crystal Structure Of Human P450 3a4 In Complex With Ketoconazole
> [mmdbId:47321]
> 5: 2NZA
> I can't find a spec that say, "return all the matching pdb's", I just get
> a
> list of id's
> and have to go get the ones I want. Still easy to automate however.
> Search criteria are here:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=structure
> I generally take the "download everything close  and sort it out locally
> approach" using custom scripts for one-off searches.
> If anyone knows the codes to download all the pdb's at once can you please
> post.

You can download whole PDB from RCSB. Goto
Click on Download, you can go with FTP download to download the full pdb.
seperate dirs are avaialable. you can write a wget based script to get the
full download.

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