<h2>Ensembl to PDB</h2>

<p>So the dataset you need is from <a href="https://www.ebi.ac.uk/pdbe/docs/sifts/quick.html" rel="nofollow noreferrer">SIFT</a>. There is one with Ensembl IDs. Majorly this also includes what chain is your peptide and what is the offset. About the latter, I actually wrote <a href="https://blog.matteoferla.com/2019/09/pdb-numbering-rollercoaster.html" rel="nofollow noreferrer">a blog post about it recently</a>.</p>

<h2>PDB download</h2>

<p>Using Python, the <a href="https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ" rel="nofollow noreferrer">Biopython PDB module</a> is very good. Although the PyMol module is more powerful. But as you want only coordinates (right?), you'd best use the former, which has a better documentation.</p>

CC BY-SA 4.0
2019-10-11T16:59:38.200Z
2019-10-11T16:59:38.200Z
Matteo Ferla
<p>Forgive me if this question is too trivial.</p>

<p>I have a list of ~700 Ensembl ID. I need to extract the protein structures of each Ensembl id. How can I do this?</p>

<p>Is there any script(python, R) so that we can download the structure from the website(like RCSB)?</p>

CC BY-SA 4.0
2019-09-16T16:03:09.323Z
Welcome, parse the pdb and then run a Pymol script. Otherwise Biopython will have a fetch which will likely pull down the pdb. Be careful of the format.
M__
CC BY-SA 4.0
2019-09-16T16:52:06.283Z
Thanks @MichaelG. As you understand, I am very novice in this field, can you be more specific with the answer. Like any link or blog.
Pratik Dutta
CC BY-SA 4.0
2019-09-16T16:56:33.137Z
Hi I've a lot on right now and I don't do Ensembl (I just use Genbank) so I'm not sure how to parse Ensembl seq -> pdb codes. Emily from Ensembl is on the forum, and might help.
M__
CC BY-SA 4.0
2019-09-16T17:05:11.447Z
Again you have to be super careful of the pdb formatting. Finally you might  want to split this into 2 questions, i.e. I think this involves 1. parsing 2. downloading.
M__
<gene><proteins><python><protein-structure>
From ensembl id to protein structure
# From ensembl id to protein structure

(Asked by: username_0 on 2019-09-16)

Forgive me if this question is too trivial.

I have a list of ~700 Ensembl ID. I need to extract the protein structures of each Ensembl id. How can I do this?

Is there any script(python, R) so that we can download the structure from the website(like RCSB)?

**Tags:** gene, proteins, python, protein-structure
> **Comments:**
> **username_1**: Welcome, parse the pdb and then run a Pymol script. Otherwise Biopython will have a fetch which will likely pull down the pdb. Be careful of the format.  
> **username_0**: Thanks @MichaelG. As you understand, I am very novice in this field, can you be more specific with the answer. Like any link or blog.  
> **username_1**: Hi I've a lot on right now and I don't do Ensembl (I just use Genbank) so I'm not sure how to parse Ensembl seq -> pdb codes. Emily from Ensembl is on the forum, and might help.  
> **username_1**: Again you have to be super careful of the pdb formatting. Finally you might  want to split this into 2 questions, i.e. I think this involves 1. parsing 2. downloading.  

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## 1 answers

### Answer by username_2 on 2019-10-11. Score: 1

## Ensembl to PDB

So the dataset you need is from [SIFT](https://www.ebi.ac.uk/pdbe/docs/sifts/quick.html). There is one with Ensembl IDs. Majorly this also includes what chain is your peptide and what is the offset. About the latter, I actually wrote [a blog post about it recently](https://blog.matteoferla.com/2019/09/pdb-numbering-rollercoaster.html).

## PDB download

Using Python, the [Biopython PDB module](https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ) is very good. Although the PyMol module is more powerful. But as you want only coordinates (right?), you'd best use the former, which has a better documentation.


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