Comparative Analysis of Techniques Oriented on the Recognition of Ligand Binding Area in Proteins - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 79

Table 4.2 The short presentation of “easy” proteins to visualize their different characteristics
PDB-ID Enzyme Biological activity Name Complex Source organism

2BYC Blue light receptor

from the BLUF
family

Signaling
protein

Dimer Rhodobacter

sphaeroides

1B1C E.C.1.6.2.4 FMN-binding domain

of human
cytochrome p450
reductase

Redox Monomer HS monomer

2IYG Dark-state structure of

the bluf domain of
the rhodobacterial
protein APPA

Signal
transduc-
tion

Dimer Rhodobacter

sphaeroides

Table 4.3 The short presentation of “hard” proteins to visualize their different characteristics

Source
organism PDB-ID Enzyme Biological activity Name Complex

3H4O Nitroreductase

family protein

Oxydoreductase
family

Monomer Clostridium

dif fi cile
630

3CB0 E.C.1.14.13.3 4-Hydroxyphe-nylacetate

3-monooxygenase

Oxidoreductase Tetramer Brucella

melitensis

3A3B Lumazine protein Luminescent

protein

Dimer Photobac-

terium
kishitanii

Table 4.4 Proteins (and their short characteristics) for which NAD + binding sites could be accu-
rately identi fi ed
PDB-ID Enzyme Biological activity Name Complex Source organism

2JHF E.C.1.1.1.1 Alcohol dehydroge-

nase E chain

Oxydoreductase Dimer Equus Caballus

horse liver

1SBY E.C.1.1.1.1 Alcohol dehydroge-

nase from
Drosophila
Lebanonensis

Oxydoreductase Dimer Scaptodrosophila

Lebanonensis

3ABI Putative uncharacter-

ized protein
ph1688

Unknown Dimer Pyrococcus

Horikoshi

Studying the graphical representation of FOD results (Fig. 4.18 ) reveals the
reasons behind the incorrect recognition of residues involved in ligand binding.
Poor results for FMN-binding residues seem to be associated with the fact that this
ligand is bound on the surface of the protein, without the need for a deep pocket.
Hydrogen bonds between the phosphate moiety and polar residues exposed on the
protein surface (responsible for stabilization of the resulting complex) do not
significantly distort the shape of the protein's hydrophobic core.