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# coding=utf-8
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
test_metal_coordination.py - Unit Tests for Metal Coordination.
"""
import unittest
from plip.structure.preparation import PDBComplex
class MetalCoordinationTest(unittest.TestCase):
"""Checks predictions against literature-validated interactions for metal coordination."""
###############################################
# Literature-validated cases from publication #
###############################################
def test_1rmd(self):
"""Zinc binding sites in RAG1 dimerization domain (1rmd)
Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 1a
"""
tmpmol = PDBComplex()
tmpmol.load_pdb("./pdb/1rmd.pdb")
bsid = "ZN:A:119"
for ligand in tmpmol.ligands:
if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Coordination by three cysteines and one histidine of the protein
metalres = [mres.restype for mres in s.metal_complexes]
self.assertEqual(metalres.count("CYS"), 3)
self.assertEqual(metalres.count("HIS"), 1)
# Zn atom with tetrahedral geometry (coordination number 4)
self.assertEqual(s.metal_complexes[0].coordination_num, 4)
self.assertEqual(s.metal_complexes[0].geometry, "tetrahedral")
def test_1rla(self):
"""Rat liver arginase, a binuclear manganese metalloenzyme (1rmd)
Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 1b
"""
tmpmol = PDBComplex()
tmpmol.load_pdb("./pdb/1rla.pdb")
bsid = "MN:A:500"
for ligand in tmpmol.ligands:
if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Coordination by one histidine, three aspartic acid residues, and one water molecule
metalres = [mres.restype for mres in s.metal_complexes]
self.assertEqual(metalres.count("HIS"), 1)
self.assertEqual(metalres.count("ASP"), 3)
self.assertEqual(metalres.count("HOH"), 1)
# Mn atom with square pyramidal geometry (coordination number 5)
self.assertEqual(s.metal_complexes[0].coordination_num, 5)
self.assertEqual(s.metal_complexes[0].geometry, "square.pyramidal")
def test_1het(self):
"""Liver alcohol deshydrogenase (1het)
Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 2
"""
tmpmol = PDBComplex()
tmpmol.load_pdb("./pdb/1het.pdb")
bsid = "ZN:A:401"
for ligand in tmpmol.ligands:
if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Coordination by four cysteines
metalres = [mres.restype + str(mres.resnr) for mres in s.metal_complexes]
self.assertEqual(set(metalres), {"CYS97", "CYS100", "CYS103", "CYS111"})
# Zn atom with tetrahedral geometry (coordination number 4)
self.assertEqual(s.metal_complexes[0].coordination_num, 4)
self.assertEqual(s.metal_complexes[0].geometry, "tetrahedral")
def test_1vfy(self):
"""Phosphatidylinositol-3-phosphate binding FYVE domain of VPS27P protein (1vfy)
Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 5
"""
tmpmol = PDBComplex()
tmpmol.load_pdb("./pdb/1vfy.pdb")
bsid = "ZN:A:300"
for ligand in tmpmol.ligands:
if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Coordination by four cysteines
metalres = [mres.restype for mres in s.metal_complexes]
self.assertEqual(set(metalres), {"CYS"})
# Zn atom with tetrahedral geometry (coordination number 4)
self.assertEqual(s.metal_complexes[0].coordination_num, 4)
self.assertEqual(s.metal_complexes[0].geometry, "tetrahedral")
def test_2pvb(self):
"""Pike parvalbumin binding calcium (2pvb)
Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 6
"""
tmpmol = PDBComplex()
tmpmol.load_pdb("./pdb/2pvb.pdb")
bsid = "CA:A:110"
for ligand in tmpmol.ligands:
if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Ca atom with square pyramidal geometry (coordination number 5)
self.assertEqual(s.metal_complexes[0].coordination_num, 5)
self.assertEqual(s.metal_complexes[0].geometry, "square.pyramidal")
def test_2q8q(self):
"""Crystal Structure of S. aureus IsdE complexed with heme (2q8q)
Reference: Grigg et al. Heme coordination by Staphylococcus aureus IsdE. (2007)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb("./pdb/2q8q.pdb")
bsid = "HEM:A:300"
for ligand in tmpmol.ligands:
if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Coordination by four nitrogens of heme itself and one additional histidine from the protein
metalres = [mres.restype for mres in s.metal_complexes]
self.assertEqual(metalres.count("HEM"), 4)
self.assertEqual(metalres.count("HIS"), 1)
# Fe atom with square pyramidal geometry (coordination number 5)
self.assertEqual(s.metal_complexes[0].coordination_num, 5)
self.assertEqual(s.metal_complexes[0].geometry, "square.pyramidal")
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