Step 1: Recall the associations of major biological databases.
\[
\boxed{
\begin{aligned}
\text{NCBI} &\rightarrow \text{GenBank}
\text{EBI} &\rightarrow \text{EMBL/ENA}
\text{ExPASy} &\rightarrow \text{Swiss-Prot (UniProt)}
\end{aligned}
}
\]
Step 2: Identify the incorrect pair.
The Protein Data Bank (PDB) is an independent international repository for three-dimensional biomolecular structures and is not associated with NCBI.
Therefore,
\[
\boxed{\text{PDB -- NCBI}}
\]
is the incorrectly matched pair.
Hence,
\[
\boxed{(D)}
\]
is the correct answer.