Does anyone have the complete chain of amino acids of Beclin1 or the complete chain of amino acids of complex for Beclin1-BCL2 (not just BH3domain of Beclin1-BCL2)? I mean the crystallography file (like pdb...)
I am going to simulate them by Gromacs.
For this type of query I suggest that you search the UNIPROT data base. For example, for the human Beclin 1 this is the UNIPROT entry, https://www.uniprot.org/uniprotkb/Q14457/entry .
When you scroll down and check the 3D structures you will see there is the electron microscopy 3D structure of a complex that contains full beclin 1 (residues 1-450), pdb ID 8SOR , plus the AlphaFold entry for the predicted structural model. HTH.
What I mean is that I need the structure of the complex of the two, not their structure individually.
You can obtain the amino acid chain of Beclin1 or Beclin1-BCL2 complex from the Protein Data Bank (PDB). Search for relevant structures, such as PDB ID 3QNQ (Beclin1-BCL2 complex), to get the full chain for your simulation in GROMACS.
All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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