I want to download 3d structures of two proteins of Acinetobacter Baumannii but am finding difficulty on PDB. can anyone guide me how to view or download 3d structures of my proteins (1. GacS-like sensor kinase protein and 2.
glutamate synthase large chain precursor)
I am afraid the structures of those proteins are not available on PDB. Not yet, at least. What makes you think they have been solved?
Experimental 3D structures are available only for a small fraction of all known proteins, and certainly not from all organisms, so you might not find the exact protein you are looking for, but maybe the structure of a homologous protein related closely enough to yield useful information.
It is easiest if you know the amino acid sequence of your protein, since names may vary, and this will tell you not only whether or not the exact protein you are looking for has been solved, but also whether a reasonably similar protein can be found which could serve as a template for homology modeling
Go to "advanced search mode"
https://www.rcsb.org/search/advanced?search=new
and do a blast search by copy-pasting the sequence in the appropriate field.
I do not think that there is a structure of the GacS-like sensor kinase protein of your organism available. The closest item in UniProt is the GacS-like sensor kinase protein of Oxytricha trifallax, https://www.uniprot.org/uniprot/J9I8W6, and a search on rcsb with that sequence yielded the cytoplasmic portion of sensor histidine kinase protein of Thermotoga maritima (2C2A) as closest hit.
Try the same with the sequence of your glutamate synthase large chain precursor.
Dear Samara Irtaza ,
Is the protein mentioned in this paper what you are looking for?
Smiline Girija, A. S. (2020). Delineating the Immuno-Dominant Antigenic Vaccine Peptides Against gacS-Sensor Kinase in Acinetobacter baumannii: An in silico Investigational Approach. Frontiers in microbiology, 11, 2078.
https://www.frontiersin.org/articles/10.3389/fmicb.2020.02078/full
Protein nr. 2 seems indeed not available in UniProt:
http://www.tartaglialab.com/bacfitbase/display?query=bacfit0000564 the available FASTA sequence can however be used to let I-Tasser make a 3-D structure prediction: https://zhanglab.ccmb.med.umich.edu/I-TASSER/ perhaps not perfect but at least you have something to work on.
Both pdb files can be put in Chimera (https://www.cgl.ucsf.edu/chimera/ ) “for the interactive visualization and analysis of molecular structures and related data”. Hope this helps you somewhat further.
Best regards.