Download Protein 3D-structure analysis

Protein 3D-structure analysis
Exercises
Practicals
Find update frequency for RCSB PDB: weekly.
When was the last update?
How many protein structures are there in wwPDB?
http://www.rcsb.org/pdb/home/home.do
http://www.ebi.ac.uk/pdbe/#m=0&h=0&e=0&r=0&l=0&a=0&w=0
Practicals
How many NEW structures were deposited in 2012 vs 2013?
At RCSB PDB, option to see results for all structures vs Protein structures only
http://www.rcsb.org/pdb/statistics/contentGrowthChart.do?content=total&seqid=100
http://www.rcsb.org/pdb/statistics/contentGrowthChart.do?content=molType-protein&seqid=100
RSSB PDB Statistics
(http://www.rcsb.org/pdb/static.do?p=general_information/pdb_statistics/index.html):
Summary Table of Released Entries
Practicals
How many structures determined by X-ray crystallography, NMR,
Electron microscopy?
Use Advanced Query at RCSB PDB
How many structures determined by X-ray crystallography, NMR,
Electron microscopy?
Facutltative: Use advanced Query at PDBe
http://www.ebi.ac.uk/pdbe-srv/view/search?search_type=advanced
Find the structure with the highest resolution at RCSB PDB
http://www.rcsb.org/pdb/static.do?p=general_information/pdb_statistics/index.html
http://www.rcsb.org/pdb/statistics/histogram.do?mdcat=refine&mditem=ls_d_res_high&minLabel=0&m
axLabel=5&numOfbars=10&name=Resolution
Alternative way:
Click here
Select the resolution
At RCSB PDB, find structures with imatinib as ligand.
How many structures contain this ligand?
What type of proteins contain this ligand?
Use advanced query. Verify using the PDB ID for imatinib=STI
Answer: Protein kinases
Amongst proteins with bound imatinib, there are structures for p38.
http://www.rcsb.org/pdb/explore/explore.do?structureId=3HEC
Find the official protein and gene name of p38
Most easily done via the UniProt entry
Find the UniProt AC for p38.
Find structures for a human protein kinase with bound ADP and a
resolution between 2 and 2.5 A:
Use advanced search, Chemical ID=ADP, then use options (Species,
Resolution, Enzyme classification, …) to filter the result
http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=7F9AA3F1&tabtoshow=Current
Resolution better than 2 A : 43 + 1 = 44 !!!
Identifiy the residues that form hydrogen bonds with the product, via
PDBsum and from the RCSB PDB website: e.g. 2IJM
http://www.ebi.ac.uk/thornton-srv/databases/cgibin/pdbsum/RunLigplot.pdf?pdb=2ijm&pdf=YES&file=ligplot02_01
and Ligand Explorer from RCSB PDB (shown below)
You can ‘BLAST’ a sequence
- directly at PDB (see next slide): you will ‘BLAST’ against protein sequences
which have a 3D structure
- You can also ‘BLAST’ against PDB at UniProt
Use the sequence of human PLK4 to find a similar structure (advanced
search tools) for chicken
Sequence: http://www.uniprot.org/uniprot/O00444.fasta
Get sequence: http://www.uniprot.org/uniprot/O00444.fasta
At RCSB PDB, find structures for proteins similar to p38
Query: p38 imatinib in main search window, choose 3HEC:
You get kinases
http://www.rcsb.org/pdb/explore/structureCluster.do?structureId=3HEC&bionumber=1
find structures for proteins similar to p38
via the DALI database (FSSP link on PDBsum page). What kind of
proteins do you recover?
http://ekhidna.biocenter.helsinki.fi/dali_server/results/20131128-0052a5d25672558cbc7d13227902797d259c/index.html
Dali: 3D structures similar to 3HEC
Sequence similarity:
Only FTO, no other ‘function’
3D structure similarity: new function: dioxygenase
The sequence identity % is low but the structures are similar
Starting with the structure for human FTO, find other proteins with similar 3Dstructure via PDB
http://www.rcsb.org/pdb/explore/structureCluster.do?structureId=3LFM
or DALI (FSSP) :
http://ekhidna.biocenter.helsinki.fi/dali_server/results/20131128-0062cd4fac4bcb593b2c2300a8425b103dcb/index.html
What kind of proteins do you find (function, taxonomy)?
Answer: dioxygenases, more specifically ALPHA-KETOGLUTARATEDEPENDENT DIOXYGENASE
Taxons: Mammalia (alkB homologs), and bacteria (alkB from E.coli)
What are their ligands?
Answer: alpha-ketoglutarate and iron
http://www.rcsb.org/pdb/explore.do?structureId=2IUW
Do an alignment based on the 3D-structure and check if the ligandbinding residues are conserved. Do this with entries from closely
related/different taxons.
A) Get the ligand-binding sites using PDBsum, UniProt annotation, or
Ligand explorer
http://www.uniprot.org/uniprot/Q9C0B1#section_features
http://www.uniprot.org/uniprot/P05050#section_features
B) Get an alignment from RCSB PDB or DALI
http://www.rcsb.org/pdb/workbench/showPrecalcAlignment.do?action=
pw_fatcat&mol=3LFM.A&mol=2IUW.A
Very low sequence identity, but secondary structure is almost the same.
Binding sites for catalytic iron (HxD and H) are boxed
Can you get the same proteins, doing a normal BLAST search with
FTO? Answer: No, they are too different
Have a look at the domain structure (InterPro) of FTO and the proteins
that you identified.
Compare InterPro lines: they are different
http://www.uniprot.org/uniprot/P05050#section_x-ref
http://www.uniprot.org/uniprot/Q9C0B1#section_x-ref
Find 3D-structures for transthyretin at RCSB PDB, then look for proteins
with similar 3D-structure
http://www.rcsb.org/pdb/explore/explore.do?structureId=1THC
Similar structure: 2H6U
What is the function of transthyretin, respectively of other proteins with
similar structure?
Have a look at the corresponding UniProt entries!
How are they classified at CATH
Use text search
http://www.cathdb.info/cathnode/2.60.40.180
NB: the proteins are too similar to be distinguished by these means
5-hydroxyisourate hydrolase is not present in primates; the structure is highly conserved.
That’s why human can have ‘gout’ …
More things to do (facultative)
Find protein structures with aspirin as ligand
Find the chemical structure for aspirin
Get all structures with the ligand aspirin. How many are there?
- Go to CHEBI, get Smiles for aspirin
- http://www.ebi.ac.uk/chebi/advancedSearchFT.do
- http://www.ebi.ac.uk/chebi/searchId.do;E5D46C3E2363F473FCE4C2
01CC2078A6?chebiId=CHEBI:15365
- Go to RCSB PDB, use advanced search (smiles)
- You can also try and draw “aspirin” using CHEBI