195 lines
8.8 KiB
ReStructuredText
195 lines
8.8 KiB
ReStructuredText
.. -*- coding: utf-8 -*-
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.. |pKa| replace:: :math:`\text{p}K_\text{a}`
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==================
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Quickstart Guide
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==================
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PROPKA can be used either via the installed script :program:`propka3`
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or as a Python module. When using the :ref:`propka3-command`, use
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.. code-block:: bash
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propka3 FILENAME
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As a module (:mod:`propka`), also provide the input filename
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.. code-block:: bash
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python -m propka FILENAME
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In both cases, additional options may be added, as described in more
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detail for the :ref:`propka3-command`.
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Predicting protein residue |pKa| values
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=======================================
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Most users run PROPKA by invoking the :program:`propka3` program with
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a PDB file as its argument; e.g., for PDB 1HPX_ (HIV-1 protease
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complexed with the inhibitor KNI-272)
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.. code-block:: bash
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propka3 1hpx.pdb
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In this example, |pKa| values of titratable protein residues and
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titratable groups of the inhibitor KNI are calculated.
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The output looks similar to the following (many lines omitted as
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"..."). It is also contained in the output file :file:`1hpx.pka` that
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is automatically written::
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propka3.2 2020-06-19
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...
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...
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Found NAR group: 1530- N1 900-KNI (B) [ 7.907 1.459 5.427] N
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Found O3 group: 1531- O1 900-KNI (B) [ 5.235 3.791 9.082] O
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Found O2 group: 1532- O3 900-KNI (B) [ 3.327 4.297 11.852] O
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Found NAM group: 1533- N2 900-KNI (B) [ 3.955 2.384 10.893] N
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Found O2 group: 1539- O6 900-KNI (B) [ 3.758 -0.629 12.111] O
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Found NAM group: 1541- N3 900-KNI (B) [ 4.496 0.982 13.492] N
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Found O2 group: 1542- O4 900-KNI (B) [ 6.324 -1.234 17.045] O
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Found OH group: 1548- O2 900-KNI (B) [ 4.949 0.934 16.427] O
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Found O2 group: 1559- O5 900-KNI (B) [ 6.746 -3.574 14.588] O
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Found NAM group: 1560- N5 900-KNI (B) [ 7.637 -4.575 16.403] N
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-------------------------------------------------------------------------------------------------------
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Calculating pKas for Conformation container 1A with 1878 atoms and 480 groups
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-------------------------------------------------------------------------------------------------------
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--------- ----- ------ --------------------- -------------- -------------- --------------
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DESOLVATION EFFECTS SIDECHAIN BACKBONE COULOMBIC
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RESIDUE pKa BURIED REGULAR RE HYDROGEN BOND HYDROGEN BOND INTERACTION
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--------- ----- ------ --------- --------- -------------- -------------- --------------
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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
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ASP 25 A -0.85 KNI O2 B -0.09 ALA 28 A 0.00 XXX 0 X
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ASP 25 A -0.84 ASP 25 B -0.04 GLY 27 B 0.00 XXX 0 X
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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
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ASP 29 A -0.28 ARG 8 B 0.00 XXX 0 X -0.47 ARG 87 A
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ASP 29 A 0.00 XXX 0 X 0.00 XXX 0 X -0.54 ARG 8 B
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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
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ASP 30 A 0.00 XXX 0 X 0.00 XXX 0 X -0.01 ARG 8 B
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ASP 30 A 0.00 XXX 0 X 0.00 XXX 0 X 0.29 ASP 29 A
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ASP 30 A 0.00 XXX 0 X 0.00 XXX 0 X -0.57 LYS 45 A
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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
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ASP 60 A -0.85 LYS 43 A 0.00 XXX 0 X -0.38 LYS 43 A
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...
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...
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...
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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
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ARG 87 B 0.00 XXX 0 X 0.00 XXX 0 X -0.19 ARG 8 A
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ARG 87 B 0.00 XXX 0 X 0.00 XXX 0 X 0.50 ASP 29 B
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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
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N+ 1 B 0.00 XXX 0 X 0.00 XXX 0 X 0.04 CYS 95 B
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N+ 1 B 0.00 XXX 0 X 0.00 XXX 0 X 0.38 C- 99 A
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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
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Coupled residues (marked *) were detected.Please rerun PropKa with the --display-coupled-residues
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or -d option for detailed information.
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--------------------------------------------------------------------------------------------------------
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SUMMARY OF THIS PREDICTION
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Group pKa model-pKa ligand atom-type
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ASP 25 A 5.07 3.80
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ASP 29 A 3.11 3.80
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ASP 30 A 4.62 3.80
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ASP 60 A 2.55 3.80
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ASP 25 B 9.28 3.80
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ASP 29 B 1.78 3.80
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ASP 30 B 4.91 3.80
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ASP 60 B 2.13 3.80
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GLU 21 A 4.78 4.50
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GLU 34 A 3.93 4.50
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GLU 35 A 3.65 4.50
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GLU 65 A 3.89 4.50
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GLU 21 B 4.73 4.50
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GLU 34 B 3.36 4.50
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GLU 35 B 4.07 4.50
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GLU 65 B 3.70 4.50
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C- 99 A 2.08 3.20
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C- 99 B 2.11 3.20
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HIS 69 A 6.98 6.50
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HIS 69 B 7.11 6.50
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CYS 67 A 9.41 9.00
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CYS 95 A 11.68 9.00
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CYS 67 B 9.82 9.00
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CYS 95 B 11.61 9.00
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TYR 59 A 9.67 10.00
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TYR 59 B 9.54 10.00
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LYS 14 A 10.43 10.50
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LYS 20 A 10.32 10.50
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LYS 43 A 11.41 10.50
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LYS 45 A 10.54 10.50
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LYS 55 A 10.42 10.50
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LYS 70 A 10.92 10.50
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LYS 14 B 10.55 10.50
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LYS 20 B 11.01 10.50
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LYS 43 B 11.43 10.50
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LYS 45 B 10.47 10.50
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LYS 55 B 10.41 10.50
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LYS 70 B 11.07 10.50
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ARG 8 A 13.96 12.50
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ARG 41 A 12.41 12.50
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ARG 57 A 14.40 12.50
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ARG 87 A 12.35 12.50
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ARG 8 B 12.76 12.50
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ARG 41 B 12.42 12.50
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ARG 57 B 13.73 12.50
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ARG 87 B 12.28 12.50
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N+ 1 A 8.96 8.00
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N+ 1 B 8.96 8.00
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KNI N1 B 4.60 5.00 NAR
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Writing 1hpx.pka
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Some of the important contents:
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- The section *Calculating pKas for Conformation container 1A with 1878 atoms and
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480 groups* lists details on the calculations for all ionizable
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residues. It indicates the considerations that went into a |pKa|
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estimate such as hydrogen bonds and Coulomb interactions. It also
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indicates if there is potentially coupling between residues.
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- Values with "XXX" placeholders are not calculated (but appear to
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maintain the formatting).
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- The section *SUMMARY OF THIS PREDICTION* lists the predicted |pKa|
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for each residue together with the model |pKa| (the "default"
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value).
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- Ligand values are labeled with the residue name of the ligand, in
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this case "KNI".
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.. todo::
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More detailed discussion of output.
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Getting help
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============
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A brief list of available options can be obtained by running PROPKA
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with no options. A longer list of options and descriptions is
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available using the :option:`propka3 --help` option:
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.. code-block:: bash
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propka3 --help
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.. links
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.. _1HPX: https://www.rcsb.org/structure/1HPX
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