Answers.Body: <p>In some protein crystallography studies, the protein crystals are grown with the substrate/ligand/inhibitor added, thus the resulting structure contains both the ligand and the protein atom coordinates. This enables studying the protein ligand complex to understand binding, specificity, mechanism of catalysis...</p>
  <p>On the other hand in some experiments protein crystals are grown without the ligand, thus the resulting structure contains coordinates just for the protein atoms.</p>
  <p>On the third hand, the lucky one, your protein, overexpressed in its natural host [sometimes even in different one], co-purify with its own natural ligand, so the resulting structure contains coordinates for both the protein atoms and the sought for ligand.</p>
  <p>To understand ligand binding the protein structure without the ligand should be compared to the structure of the protein-ligand complex.</p>
  <p>Many published papers report both types of crystals.</p>
  <p>For example the crystal structure of pectin methylesterase in complex with hexasaccharide VI: <a href="https://www.rcsb.org/structure/2NTP" rel="nofollow noreferrer">2NTP</a> is from the publication <a href="https://doi.org/10.1038/sj.emboj.7601816" rel="nofollow noreferrer">https://doi.org/10.1038/sj.emboj.7601816</a> which is the source of six other structures. These structures include the enzyme with different substrates, as well as the active site mutants (D178A) all of which were prepared to understand the molecular basis of substrate specificity. The conclusion after studying all of the mentioned structures is nicely summed in the sentence from the abstract:</p>
  <blockquote>
  <p>The preferential binding of methylated sugar residues upstream of the catalytic site, and demethylated residues downstream, drives the enzyme along the pectin molecule and accounts for the sequential pattern of demethylation produced by both bacterial and plant PMEs.</p>
  </blockquote>
  
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Body: <p>I am a newbie in bioinformatics. In PDB, while searching for proteins, I sometimes get protein with ligand, such as PDB ID 1J1Z. In cases I get pure protein structure, in some cases I get protein-with ligand.</p>
  <p>I am having hard time understanding why I can have ligand in PDB structure. I am PDB is supposed to give me pure protein 3D structure. Then how can we have ligand in protein structure??</p>
  <p>And sorry if my question is stupid.</p>
  
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Tags: <protein-structure><pdb>
Title: Protein-Ligand in PDB
ThreadText: # Protein-Ligand in PDB
  
  (Asked by: username_0 on 2022-04-23)
  
  I am a newbie in bioinformatics. In PDB, while searching for proteins, I sometimes get protein with ligand, such as PDB ID 1J1Z. In cases I get pure protein structure, in some cases I get protein-with ligand.
  
  I am having hard time understanding why I can have ligand in PDB structure. I am PDB is supposed to give me pure protein 3D structure. Then how can we have ligand in protein structure??
  
  And sorry if my question is stupid.
  
  **Tags:** protein-structure, pdb
  
  > **Comments:**
  > **username_1**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-04-23. Score: 2 | Accepted answer
  
  In some protein crystallography studies, the protein crystals are grown with the substrate/ligand/inhibitor added, thus the resulting structure contains both the ligand and the protein atom coordinates. This enables studying the protein ligand complex to understand binding, specificity, mechanism of catalysis...
  
  On the other hand in some experiments protein crystals are grown without the ligand, thus the resulting structure contains coordinates just for the protein atoms.
  
  On the third hand, the lucky one, your protein, overexpressed in its natural host [sometimes even in different one], co-purify with its own natural ligand, so the resulting structure contains coordinates for both the protein atoms and the sought for ligand.
  
  To understand ligand binding the protein structure without the ligand should be compared to the structure of the protein-ligand complex.
  
  Many published papers report both types of crystals.
  
  For example the crystal structure of pectin methylesterase in complex with hexasaccharide VI: [2NTP](https://www.rcsb.org/structure/2NTP) is from the publication <https://doi.org/10.1038/sj.emboj.7601816> which is the source of six other structures. These structures include the enzyme with different substrates, as well as the active site mutants (D178A) all of which were prepared to understand the molecular basis of substrate specificity. The conclusion after studying all of the mentioned structures is nicely summed in the sentence from the abstract:
  
  > The preferential binding of methylated sugar residues upstream of the catalytic site, and demethylated residues downstream, drives the enzyme along the pectin molecule and accounts for the sequential pattern of demethylation produced by both bacterial and plant PMEs.
  
  > **Comments:**
  > **username_1**: Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers [in the help center](/help/how-to-answer).  
  
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