Load the 1XDN files
Download 1XDN files
(receptor.pdb and ligand.pdb) into BINANA to answer this and the following questions.

What type of interaction does ASN92 form with the ligand?

Question

Load the 1XDN files 
Download 1XDN files
(receptor.pdb and ligand.pdb) into BINANA to answer this and the following questions.

What type of interaction does ASN92 form with the ligand?

BlackTom AI · Accepted Answer

Question restatement: You are loading 1XDN receptor and ligand files into BINANA and asked to identify the type of interaction ASN92 forms with the ligand.

Given answer: Hydrogen bond.

Without a provided list of answer options to compare against, we focus on what is known about ASN92’s potential interactions with a bound ligand. ASN (asparagine) has a polar amide side chain (–CONH2) that contains both hydrogen-bond donor and acceptor capabilities: the carbonyl oxygen can accept a hydrogen bond, while the amide nitrogens can donate hydrogen bonds. This makes ASN residues common participants in hydrogen-bond networks with ligands, especially when functional groups on the ligand present donors (–NH, –OH, etc.) or acceptors (carbonyls, nitro groups, ether oxygens, etc.).

Detailed reasoning about hydrogen bonding possibilities: first, assess whether ASN92’s backbone or side-chain atoms could participate. The side-chain carbonyl oxygen (OD) acts as a hydrogen-bond acceptor; the amide nitrogens (ND2, ND1) can donate hydrogen bonds if a suitable hydrogen donor is present on the ligand. Additionally, the backbone amide group nearby could, in some cases, engage in hydrogen bonding with the ligand through its N–H as donor or carbonyl O as acceptor, though FUNC/geometry in BINANA typically emphasizes side-chain interactions for residue-ligand contacts.

Why hydrogen bonding is a plausible interaction here: BINANA often reports hydrogen bonds between receptor residues and ligand when appropriate donor–acceptor geometry and distance criteria are met (roughly 2.5–3.5 Å for H-bonds, with favorable angle). An asparagine side chain is well-suited to form such interactions with various functional groups on the ligand, including carbonyls, hydroxyls, carboxylates, or amines that can participate as donors.

Why other interaction types (if present in the dataset) might be less likely in this specific case: hydrophobic contacts require nonpolar surface areas to align, which may be limited around ASN92 if it resides in a polar region; ionic interactions would require charged groups on the ligand and an oppositely charged site on the residue, which is less typical for an asparagine’s neutral side chain under physiological pH; aromatic stacking or cation–pi interactions depend on nearby aromatic residues or cationic centers, which ASN92 alone does not provide.

In summary, the combination of ASN92’s hydrogen-bond donor and acceptor capabilities and common ligand functional groups makes hydrogen bonding a highly plausible interaction type between ASN92 and the ligand in BINANA analyses.

2254 BIOSC 1544 SEC1000 Homework: BINANA

Load the 1XDN files Download 1XDN files (receptor.pdb and ligand.pdb) into BINANA to answer this and the following questions. What type of interaction does ASN92 form with the ligand?

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