2. Sequence: PFAM
Used example:
Database of protein domain families. It is based on manually curated alignments of known domains. This alignments are stored in a form of Hidden Markov Models (HMM). This way, if a sequence aligns with one of these profiles, we would interpret that this sequence contains the domain defined by the HMM profile.

3. Sequence: PFAM
Only those regions in the query sequence that align with a hmm profile in the database are shown 3 4 1 2

4. Sequence: PFAM
Name ID

5. Sequence: PFAM

6. Sequence: PFAM
This family is similar to others and they are grouped in a “Clan”

7. Sequence: PFAM
You can visualize or download many different alignments for proteins in this family:
Seed alignment is the one used to generate the HMM profile that define this domain family.

8. Sequence: PFAM
Using the “Logo” the conservation degree for each position in the domain can easily be seen:

9. Sequence: PFAM
The HMM profile derived from the seed alignment which defines this domain can be downloaded. We can use it to create highly reliable multiple alignments

10. Sequence: PFAM Proteins with solved structures containing this domain.
(Take good care with residue numbers, they can be wrong)

11. Structure: PDB THE Database
PDB stores proteins (and DNA, lipids, small molecules …) with their structures solved. These means that we know the coordinates X,Y and Z of their atoms. So we can see their “shape” and KNOW which residues are buried, which are exposed, the distance between them, their interactions, etc.
Every structure deposited has a 4 digit code which starts with a number and then has 3 other characters which are normally letters. They currently have no meaning, although the first ones did (Ex 4CPA = CarboxyPeptidase A)
Apart from the coordinates it also has information derived from them, from the state in which the protein was when preparing it for solving its structure or the experiment conditions when its structure was solved (catalytic, binding and allosteric sites, ligands, secondary structures, mutations, etc.)

12. Structure: PDB THE Database We will use 3IGN structure as an example 12

13. Structure: PDB Structure Summary General Data
View the structure interactively (rotate, zoom, cartoons, surface, etc
Publications:
View this pubmed entry
Search PDB by this pubmed reference

14. Structure: PDB Structure Summary
All proteins (chains) present in this structure
(links to uniprot)
Different known and predicted features
Ligands present in this structure (their structure is also solved)

15. Structure: PDB Structure Summary
We will download the structure in a text file with “pdb” format (the most standard, all software reads this format)
We can download the structure as it was solved in the experiment (PDB format) or
As it works in the nature (Biological Assembly). We can have several structures here because sometimes this is not clear or if the protein works as a monomer but it was solved as a multimer

16. Structure: PDB Structure Sunmary
We have to take care when downloading the “FASTA” sequence, this is not necessarily nor the protein sequence nor the sequence with the X,Y,Z coordinates for its atoms in the pdb file. This is the sequence that the experimentalist who solved the structure used.
It can contain mutations, be just a fragment or include tags used for purification that are not present in the real protein.
At the same time, perhaps not all atoms and / or all residues could have the X,Y,Z coordinates determined, so not all the AA in the sequence have their structure solved

17. Structure: PDB Structure Sunmary
What can be downloaded can also be displayed

18. Structure: PDB PDB file This : https://files.rcsb.org/view/3IGN.pdb#
#Field | Column | FORTRAN |
# No. | range | format | Description
# 1. | | A6 | Record ID (eg ATOM, HETATM)
# 2. | | I5 | Atom serial number
# - | | 1X | Blank
# 3. | | A4 | Atom name (eg " CA " , " ND1")
# 4. | | A1 | Alternative location code (if any)
# 5. | | A3 | Standard 3-letter amino acid code for residue
# - | | 1X | Blank
# 6. | | A1 | Chain identifier code
# 7. | | I4 | Residue sequence number
# 8. | | A1 | Insertion code (if any)
# - | | 3X | Blank
# 9. | | F8.3 | Atom's x-coordinate
# 10. | | F8.3 | Atom's y-coordinate
# 11. | | F8.3 | Atom's z-coordinate
# 12. | | F6.2 | Occupancy value for atom
# 13. | | F6.2 | B-value (thermal factor)
# - | | 1X | Blank
# 14. | | I3 | Footnote number # # # #
#ATOM N GLY C
#ATOM P POM
#ATOM SE MSE A SE
Is a pdb file, it contains a header with all the information present in the web page (sequence, ligands, binding site, Uniprot code, etc.)
And the XYZ coordinates for the atoms of the molecules present in the structure
with the following format:

19. Structure: PDB
Annotations

20. Structure: PDB Sequence
Here we can view the sequence for all chains and all features annotated in the pdb file

21. Structure: PDB Sequence Change the sequence displayed:
Sequence used by the experimentalist to solve this structure
Sequence in Uniprot for this protein
Mouse over a residue to see the residue and its number (numeration in PDB is not necessary the position in the sequence) this can be a cause for confusion

22. Structure: PDB Sequence similarity
In this case no other protein in the PDB has a similar sequence over 50%

23. Structure: PDB Structure similarity
Here we can see those structures that have a domain similar to any domain that ours has.
In this case 3IGN has one structural domain.
No precomputed results have been found for our structure, so the results for the most similar one (sequence based) are shown.

24. Structure: PDB Pairwaise Structure superposition1 2
We have seen that 4ZVF is used as a structure representative for 3IGN despide having low sequence identity (40%). We can superpose both structures here. 3 6 4 7 5

25. Structure: PDB
Pairwaise Structure superposition 1 2 3 6 4 7 5

26. Structure: PDB Pairwaise Structure superposition
We can see that both structures are very similar (RMSD=1.52A) despite having a low sequence identity (36.9%)

27. Structure: PDB Pairwaise Structure superposition
We can visualize the sequence alignment derived from the structure superposition

28. Structure: PDB Advanced search1
Many search parameters can be combined to refine a search.
Results can be retrieved for structures or for ligands.
Help file: 2 3 4 6 5 7

29. Structure: PDB
Advanced search

30. Structure: PDB Ligand search
We can search for a ligand drawing its structure, searching by its name or by its formula 1 2 3 4 5

31. Structure: PDB
Ligand search