Missing residues in protein structures of DNA-PKcsΒΆ

This script creates two bars, each indicating gaps in the structure of DNA-PKcs. The top bar indicates the missing residues in a recent crystal structure (PDB: 5LUQ), the bottom bar indicates missing residues in a recent cryo-EM structure (PDB: 5W1R).

  • Green: Space-resolved residues

  • Yellow: Residues with merely polyalanine annotation

  • Red: Unresolved residues

5luq, 5w1r
# Code source: Patrick Kunzmann
# License: BSD 3 clause

from tempfile import gettempdir
import biotite.structure as struc
import biotite.structure.io as strucio
import biotite.database.rcsb as rcsb
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
import numpy as np

def plot_gaps(pdb_id, chain_id, ax):
    # Download and parse structure file
    path = rcsb.fetch(pdb_id, "mmtf", gettempdir())
    atom_array = strucio.load_structure(path)
    # Consider only one chain
    atom_array = atom_array[atom_array.chain_id == chain_id]
    # Array for saving the 'green', 'yellow' and 'red' state
    states = np.zeros(atom_array.res_id[-1], dtype=int)
    for i in range(len(states)):
        # Get array for only one residue ID
        residue = atom_array[atom_array.res_id == i+1]
        if len(residue) == 0:
            # not existing
            states[i] = 0
        elif residue.res_name[0] == "UNK":
            # exisiting but polyalanine
            states[i] = 1
            # existing
            states[i] = 2

    # Find the intervals for each state
    state_intervals = []
    curr_state = None
    curr_start = None
    for i in range(len(states)):
        if curr_start is None:
            curr_start = i
            curr_state = states[i]
            if states[i] != states[i-1]:
                state_intervals.append((curr_start, i, curr_state))
                curr_start = i
                curr_state = states[i]
    state_intervals.append((curr_start, i, curr_state))

    # Draw the state intervals as colored rectangles
    for interval in state_intervals:
        start = interval[0]
        stop = interval[1]
        state = interval[2]
        if state == 0:
            color = "firebrick"
        elif state == 1:
            color = "gold"
        elif state == 2:
            color = "forestgreen"
        ax.add_patch(Rectangle((start+1-0.5, 0), stop-start, 1,
                                edgecolor="None", facecolor=color))
    # Some other visual stuff
    ax.set_xlim(0.5, len(states) + 0.5)
    ax.set_ylim(0, 2)

fig = plt.figure(figsize=(8.0, 2.5))
ax = fig.add_subplot(211)
ax.set_title("5luq", loc="left")
plot_gaps("5luq", "A", ax)
ax = fig.add_subplot(212)
ax.set_title("5w1r", loc="left")
plot_gaps("5w1r", "A", ax)
ax.set_xlabel("$Residue \ number$")

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