2. Quickstart Guide¶
PROPKA can be used either via the installed script propka3 or as a Python module. When using the propka3 command, use
propka3 FILENAME
As a module (propka), also provide the input filename
python -m propka FILENAME
In both cases, additional options may be added, as described in more detail for the propka3 command.
2.1. Predicting protein residue \(\text{p}K_\text{a}\) values¶
Most users run PROPKA by invoking the propka3 program with a PDB file as its argument; e.g., for PDB 1HPX (HIV-1 protease complexed with the inhibitor KNI-272)
propka3 1hpx.pdb
In this example, \(\text{p}K_\text{a}\) values of titratable protein residues and titratable groups of the inhibitor KNI are calculated.
The output looks similar to the following (many lines omitted as
“…”). It is also contained in the output file 1hpx.pka that
is automatically written:
propka3.2 2020-06-19
...
...
Found NAR group: 1530- N1 900-KNI (B) [ 7.907 1.459 5.427] N
Found O3 group: 1531- O1 900-KNI (B) [ 5.235 3.791 9.082] O
Found O2 group: 1532- O3 900-KNI (B) [ 3.327 4.297 11.852] O
Found NAM group: 1533- N2 900-KNI (B) [ 3.955 2.384 10.893] N
Found O2 group: 1539- O6 900-KNI (B) [ 3.758 -0.629 12.111] O
Found NAM group: 1541- N3 900-KNI (B) [ 4.496 0.982 13.492] N
Found O2 group: 1542- O4 900-KNI (B) [ 6.324 -1.234 17.045] O
Found OH group: 1548- O2 900-KNI (B) [ 4.949 0.934 16.427] O
Found O2 group: 1559- O5 900-KNI (B) [ 6.746 -3.574 14.588] O
Found NAM group: 1560- N5 900-KNI (B) [ 7.637 -4.575 16.403] N
-------------------------------------------------------------------------------------------------------
Calculating pKas for Conformation container 1A with 1878 atoms and 480 groups
-------------------------------------------------------------------------------------------------------
--------- ----- ------ --------------------- -------------- -------------- --------------
DESOLVATION EFFECTS SIDECHAIN BACKBONE COULOMBIC
RESIDUE pKa BURIED REGULAR RE HYDROGEN BOND HYDROGEN BOND INTERACTION
--------- ----- ------ --------- --------- -------------- -------------- --------------
ASP 25 A 5.07* 100 % 4.30 617 0.19 0 -0.85 KNI O4 B -0.63 GLY 27 A 0.07 ASP 29 A
ASP 25 A -0.85 KNI O2 B -0.09 ALA 28 A 0.00 XXX 0 X
ASP 25 A -0.84 ASP 25 B -0.04 GLY 27 B 0.00 XXX 0 X
ASP 29 A 3.11 50 % 1.20 420 0.13 0 -0.68 ARG 87 A 0.00 XXX 0 X -0.04 LYS 45 A
ASP 29 A -0.28 ARG 8 B 0.00 XXX 0 X -0.47 ARG 87 A
ASP 29 A 0.00 XXX 0 X 0.00 XXX 0 X -0.54 ARG 8 B
ASP 30 A 4.62 59 % 1.30 446 0.00 0 -0.11 LYS 45 A 0.00 XXX 0 X -0.07 ARG 87 A
ASP 30 A 0.00 XXX 0 X 0.00 XXX 0 X -0.01 ARG 8 B
ASP 30 A 0.00 XXX 0 X 0.00 XXX 0 X 0.29 ASP 29 A
ASP 30 A 0.00 XXX 0 X 0.00 XXX 0 X -0.57 LYS 45 A
ASP 60 A 2.55 0 % 0.41 249 0.00 0 -0.40 THR 74 A 0.00 XXX 0 X -0.02 LYS 45 A
ASP 60 A -0.85 LYS 43 A 0.00 XXX 0 X -0.38 LYS 43 A
...
...
...
ARG 87 B 12.28 45 % -1.40 407 0.00 0 0.77 ASP 29 B 0.00 XXX 0 X 0.10 ASP 30 B
ARG 87 B 0.00 XXX 0 X 0.00 XXX 0 X -0.19 ARG 8 A
ARG 87 B 0.00 XXX 0 X 0.00 XXX 0 X 0.50 ASP 29 B
N+ 1 B 8.96 0 % -0.39 235 0.00 0 0.85 C- 99 A 0.00 XXX 0 X 0.07 CYS 67 B
N+ 1 B 0.00 XXX 0 X 0.00 XXX 0 X 0.04 CYS 95 B
N+ 1 B 0.00 XXX 0 X 0.00 XXX 0 X 0.38 C- 99 A
KNI N1 B 4.60 0 % -0.36 273 0.00 0 0.00 XXX 0 X 0.00 XXX 0 X -0.03 ARG 8 A
Coupled residues (marked *) were detected.Please rerun PropKa with the --display-coupled-residues
or -d option for detailed information.
--------------------------------------------------------------------------------------------------------
SUMMARY OF THIS PREDICTION
Group pKa model-pKa ligand atom-type
ASP 25 A 5.07 3.80
ASP 29 A 3.11 3.80
ASP 30 A 4.62 3.80
ASP 60 A 2.55 3.80
ASP 25 B 9.28 3.80
ASP 29 B 1.78 3.80
ASP 30 B 4.91 3.80
ASP 60 B 2.13 3.80
GLU 21 A 4.78 4.50
GLU 34 A 3.93 4.50
GLU 35 A 3.65 4.50
GLU 65 A 3.89 4.50
GLU 21 B 4.73 4.50
GLU 34 B 3.36 4.50
GLU 35 B 4.07 4.50
GLU 65 B 3.70 4.50
C- 99 A 2.08 3.20
C- 99 B 2.11 3.20
HIS 69 A 6.98 6.50
HIS 69 B 7.11 6.50
CYS 67 A 9.41 9.00
CYS 95 A 11.68 9.00
CYS 67 B 9.82 9.00
CYS 95 B 11.61 9.00
TYR 59 A 9.67 10.00
TYR 59 B 9.54 10.00
LYS 14 A 10.43 10.50
LYS 20 A 10.32 10.50
LYS 43 A 11.41 10.50
LYS 45 A 10.54 10.50
LYS 55 A 10.42 10.50
LYS 70 A 10.92 10.50
LYS 14 B 10.55 10.50
LYS 20 B 11.01 10.50
LYS 43 B 11.43 10.50
LYS 45 B 10.47 10.50
LYS 55 B 10.41 10.50
LYS 70 B 11.07 10.50
ARG 8 A 13.96 12.50
ARG 41 A 12.41 12.50
ARG 57 A 14.40 12.50
ARG 87 A 12.35 12.50
ARG 8 B 12.76 12.50
ARG 41 B 12.42 12.50
ARG 57 B 13.73 12.50
ARG 87 B 12.28 12.50
N+ 1 A 8.96 8.00
N+ 1 B 8.96 8.00
KNI N1 B 4.60 5.00 NAR
Writing 1hpx.pka
Some of the important contents:
The section Calculating pKas for Conformation container 1A with 1878 atoms and 480 groups lists details on the calculations for all ionizable residues. It indicates the considerations that went into a \(\text{p}K_\text{a}\) estimate such as hydrogen bonds and Coulomb interactions. It also indicates if there is potentially coupling between residues.
Values with “XXX” placeholders are not calculated (but appear to maintain the formatting).
The section SUMMARY OF THIS PREDICTION lists the predicted \(\text{p}K_\text{a}\) for each residue together with the model \(\text{p}K_\text{a}\) (the “default” value).
Ligand values are labeled with the residue name of the ligand, in this case “KNI”.
2.2. Getting help¶
A brief list of available options can be obtained by running PROPKA
with no options. A longer list of options and descriptions is
available using the propka3 --help option:
propka3 --help