Protein Data Bank, a publically available database of molecular structures of proteins

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How to find a PDB structure of a protease with a peptide like inhibitor

I wonder how, for purposes of just illustrating some concepts like substrate alignment in the catalytic triad active site, I can quickly and efficiently find a protease structure (irrelevant of what ...
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155 views

Protein structures given in PDB and SNP's

There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB ...
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PQR files make from pdb2pqr are different to GROMACS

I have a pdb file and I would like to make a pqr one. In GROMACS, I use editconf -mead to produce pqr, with topol.top taken from pdb2gmx or use it to produce pdb file, then use pdb2pqr. Which one is ...
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83 views

Color van der waals bonds in swiss PdbViewer

I'm trying to color certain amino acid's van der waals bonds as in the following picture: can anybody please describe the steps to accomplish that?
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PDB file for Osteopontin (SPP1)

I am looking for PDB file for Osteopontin (SPP1). The entry- 3CXD shows the structure of an Osteopontin antibody, not of the protein itself. Thanks
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46 views

How to parse SCOP parseable files PDB residue identifiers?

I am trying to parse the SCOP parseable files, specifically dir.des.scop.txt ver 1.75. But, I have been facing problems with the PDB residue identifiers in the file. This is a tab limited file and the ...
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1answer
44 views

Where can I find pdb files for macromolecules like receptors?

I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.
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140 views

Protein data bank syntax: Can two protein secondary structures “overlap”?

I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file: ...
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Compressing structural information in PDB files

There seems to be a lot of redundancy in PDB files. These files can of course be compressed with general-purpose compression programs like gzip, but I can't help but imagine that these tools are ...
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57 views

Parse PDB using DSR-PDB Library

I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose. I've encountered a problem. This library interprets CD1 atom of ILE ...
5
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106 views

How do I prepare a PDB for submission to the Protein Data Bank?

I have a couple structures that are nearly ready to be deposited in the PDB. Out of curiosity, I ran them through the ADIT's precheck tool and they failed with one error after another, as I lacked ...
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How can I pare down a PDB file in Python to only include specific residues?

I'm trying to make a script that will take a MTZ file (reflections), convert it into a CCP4 map, then pare that map down to only encompass a desired area to cut down on the size of my PyMol session ...