The practical exercises will be performed using two software tools – ValidatorDB and PDB validation reports. These two tools cover all of the validation analyses mentioned above (Figure 4.1) and they provide precalculated and weekly updated results for the whole of PDB. A usage of ValidatorDB is shown in the solution of demo exercises 1, 4 and 7. A work with validation reports is introduced in the demo exercises 8 and 10. When you want to validate your structures, use MotiveValidator and Mogul.
1. Demo exercise: Detecting of problematic ligands in nipah G attachmentglycoprotein
Validate all the ligands in the nipah G attachment glycoprotein (PDB ID 3d12).
Detect which of them have missing atoms or wrong chirality and describe where
the validation issues are (which ligand and which atom).
2. Validation of sucrose (SUC) in Plant Photosystem I – missing atoms
Validate a molecule of sucrose (SUC, residue ID 1226) in Plant Photosystem I
(PDB ID 2wsc). Detect which atom is missing.
3. Validation of β-carotene (BCR) in Plant Photosystem I – missing rings
Validate a molecule of β-carotene (BCR) in Photosystem I (PDB ID 4rku).
Detect which atoms within the ring of this molecule are missing.
4. Demo exercise: Validation of maltose (MAL) ligands in Protein Data Bank– missing atoms and rings
Detect all maltose (MAL) ligands in Protein Data Bank which have missing
atoms and rings.
5. Detection of atom substitution in biotin (BTN) from 50S Complex (PDB ID1kqs)
Validate biotin (BTN) from 50S Complex (PDB ID 1kqs) and detect which
atom is substituted.
6. Detection of chirality problems in all sialic acids (SIA) from Protein DataBank
Validate all sialic acids from PDB and identify the atoms of this molecule at
which chirality errors occur.
7. Demo exercise: Detection of chirality problems in testosterone derivatives
Validate all samples of these testosterone derivatives: 5-beta-dihydrotestosterone
(BDT), 5-α-dihydrotestosterone (DHT), epi-testosterone (FFA), testosterone (TES)
and testosterone hemisuccinate (TH2). Detect if there are any samples with chir
8. Demo exercise: Obtaining of structure validation data for a rhodostomin
Obtain information about structure quality for a rhodostomin (PDB ID 4rqg),
a) How many clashes are there in the structure?
b) Which atom clashes are the closest?
c) How many bond length outliers are in the structure?
d) Which bond length outlier is the highest?
e) How many bond angle outliers are in the structure?
f) Which bond angle outlier is the highest?
9. Obtaining of structure validation data for a mutant of cytochrome P450cam
Obtain information about structure quality for a mutant of cytochrome P450cam
(PDB ID 2h7s), specifically:
a) How many clashes are in the structure?
b) Are there any atoms closer than 1 A? ˚
c) How many bond length outliers are there in the structure?
d) Are there any bond length outliers > 0.3 A? ˚
e) How many bond angle outliers are there in the structure?
f) Which bond angle outlier > 20◦?
10. Demo exercise: Understanding of PDB validation reports summary criteriafor oxy-hemoglobine in methanol
Protein Data Bank in Europe uses summary quality criteria to summarize val
idation information about the structure. The summary criteria are: Clashscore,
Ramachandran outliers, sidechain outliers, RSRZ outliers.
Obtain summary criteria for oxy-hemoglobine in methanol (PDB ID 1lfz) and
then learn more about their meaning.