<p>Insulin, perhaps?</p>
<p><a href="https://www.rcsb.org/structure/1trz" rel="nofollow noreferrer">https://www.rcsb.org/structure/1trz</a></p>
<p>From <a href="https://pdb101.rcsb.org/motm/14" rel="nofollow noreferrer">here</a>:</p>
<blockquote>
<p>Insulin is a perfect molecule for exploring protein structure. It is small enough that you can display all of the atoms and still have a picture that is not too confusing. Human insulin is pictured here, using entry 1trz. This structure, like many other insulin structures, includes a hexameric complex of the hormone, and only one monomer (composed of one A-chain and one B-chain) is shown here. In the structure, you can see many of the key features that stabilize protein structure. Carbon-rich amino acids, like leucine and isoleucine, cluster in the middle of the molecule, forming a hydrophobic core, and the surface is covered with charged amino acids like arginine and glutamate that interact favorably with the surrounding water. Also notice the three disulfide bridges between cysteine amino acids, which stabilize this tiny protein.</p>
</blockquote>

CC BY-SA 4.0
2022-07-01T14:59:26.007Z
Although an excellent, canonical example ... it does have the slight downside of not having any sheet structure. It does have an bit of extended chain (shown as an isolated strand in the RCSB link). Maybe crambin (http://www.cathdb.info/version/latest/domain/1ejgA00) ?
gilleain
CC BY-SA 4.0
2022-07-01T19:52:09.557Z
Can you please add this comment as a separate answer?
gringer
CC BY-SA 4.0
2022-06-30T04:19:26.177Z
2022-06-30T04:19:26.177Z
gringer
<p>Although Insulin is a great, well studied example of a small structure it does have the slight downside of not having any sheet structure in the monomer. There is a small cross-chain sheet between residues 24-26 in both the B and D chains (from <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/1zni/" rel="nofollow noreferrer">https://www.ebi.ac.uk/pdbe/entry/pdb/1zni/</a> ).</p>
<p>Another possibility might be crambin (<a href="http://www.cathdb.info/version/latest/domain/1ejgA00" rel="nofollow noreferrer">http://www.cathdb.info/version/latest/domain/1ejgA00</a>) which does have a small antiparallel sheet, although it is tiny at only 2 residues per strand.</p>
<p>A more general approach might be to use something like the top2018 structure set from the Richardson lab (<a href="https://zenodo.org/record/5777651#.YtQB59LMJH4" rel="nofollow noreferrer">https://zenodo.org/record/5777651#.YtQB59LMJH4</a>) . I used the top500 back in the day, and they are a high-quality set of structures.</p>

CC BY-SA 4.0
2022-07-17T14:14:18.823Z
2022-07-17T14:14:18.823Z
gilleain
<p>I am developing a bioinformatics framework only for learning purposes. I want to calculate --</p>
<ol>
<li>dihedral angles</li>
<li>detect H, E, and C components</li>
<li>detect Hydrogen bonds</li>
<li>etc.</li>
</ol>
<p>Therefore, I want a PDB file that represents a protein with a small chain but is complex enough for me to experiment with.</p>
<p>Can you suggest such a PDB file?</p>

CC BY-SA 4.0
2022-06-30T14:45:13.523Z
detect H, E, and C components ? what are they ?
pippo1980
CC BY-SA 4.0
2022-06-30T16:35:20.450Z
@pippo1980, Helix, Sheet, Coil.
user366312
CC BY-SA 4.0
2022-06-30T18:22:48.777Z
was missing the E. What about Turns  and Loops
pippo1980
CC BY-SA 4.0
2022-06-30T18:28:52.993Z
@pippo1980, Firstly, I am only talking about secondary structures (so, turns are not discussed). Secondly, Loops and Coils are mostly synonymous.
user366312
CC BY-SA 4.0
2022-07-01T14:53:04.183Z
Turns may not be SSEs (although they are related) but it may be worthwhile detecting them anyway, as it is fairly simple to check for a Calpha-Calpha distance less than 4Å
gilleain
<pdb>
Example of a small but moderately complex PDB file?
# Example of a small but moderately complex PDB file?

(Asked by: username_0 on 2022-06-29)

I am developing a bioinformatics framework only for learning purposes. I want to calculate --

1. dihedral angles
2. detect H, E, and C components
3. detect Hydrogen bonds
4. etc.

Therefore, I want a PDB file that represents a protein with a small chain but is complex enough for me to experiment with.

Can you suggest such a PDB file?

**Tags:** pdb
> **Comments:**
> **username_1**: detect H, E, and C components ? what are they ?  
> **username_0**: @pippo1980, Helix, Sheet, Coil.  
> **username_1**: was missing the E. What about Turns  and Loops  
> **username_0**: @pippo1980, Firstly, I am only talking about secondary structures (so, turns are not discussed). Secondly, Loops and Coils are mostly synonymous.  
> **username_2**: Turns may not be SSEs (although they are related) but it may be worthwhile detecting them anyway, as it is fairly simple to check for a Calpha-Calpha distance less than 4Å  

---

## 2 answers

### Answer by username_2 on 2022-07-17. Score: 4 | Accepted answer

Although Insulin is a great, well studied example of a small structure it does have the slight downside of not having any sheet structure in the monomer. There is a small cross-chain sheet between residues 24-26 in both the B and D chains (from <https://www.ebi.ac.uk/pdbe/entry/pdb/1zni/> ).

Another possibility might be crambin (<http://www.cathdb.info/version/latest/domain/1ejgA00>) which does have a small antiparallel sheet, although it is tiny at only 2 residues per strand.

A more general approach might be to use something like the top2018 structure set from the Richardson lab (<https://zenodo.org/record/5777651#.YtQB59LMJH4>) . I used the top500 back in the day, and they are a high-quality set of structures.


---

### Answer by username_3 on 2022-06-30. Score: 2

Insulin, perhaps?

<https://www.rcsb.org/structure/1trz>

From [here](https://pdb101.rcsb.org/motm/14):

> Insulin is a perfect molecule for exploring protein structure. It is small enough that you can display all of the atoms and still have a picture that is not too confusing. Human insulin is pictured here, using entry 1trz. This structure, like many other insulin structures, includes a hexameric complex of the hormone, and only one monomer (composed of one A-chain and one B-chain) is shown here. In the structure, you can see many of the key features that stabilize protein structure. Carbon-rich amino acids, like leucine and isoleucine, cluster in the middle of the molecule, forming a hydrophobic core, and the surface is covered with charged amino acids like arginine and glutamate that interact favorably with the surrounding water. Also notice the three disulfide bridges between cysteine amino acids, which stabilize this tiny protein.

> **Comments:**
> **username_2**: Although an excellent, canonical example ... it does have the slight downside of not having any sheet structure. It does have an bit of extended chain (shown as an isolated strand in the RCSB link). Maybe crambin (http://www.cathdb.info/version/latest/domain/1ejgA00) ?  
> **username_3**: Can you please add this comment as a separate answer?  

---

