Load the 4EZ3 files
Download 4EZ3 files
(receptor.pdb and ligand.pdb) into BINANA to answer this and the following questions.

What type of interaction does ASP86 form with the ligand?

Question

Load the 4EZ3 files 
Download 4EZ3 files
(receptor.pdb and ligand.pdb) into BINANA to answer this and the following questions.

What type of interaction does ASP86 form with the ligand?

BlackTom AI · Accepted Answer

Question restatement: The task asks, after loading the 4EZ3 files (receptor.pdb and ligand.pdb) into BINANA, what type of interaction does ASP86 form with the ligand? The provided answer option is: Hydrogen bond.

Given only one answer option is provided, we will evaluate it in context.

- Option: Hydrogen bond. This choice proposes that ASP86 forms a hydrogen bond with the ligand. In protein–ligand interactions, aspartate (ASP) has functional groups (carboxylate) that can donate or accept hydrogen bonds depending on the protonation state and local environment. If ASP86 is in a state where its carboxylate oxygens participate as a hydrogen bond acceptor or if there is a protonated carboxyl group in a specific microenvironment, a hydrogen bond interaction with an appropriate hydrogen-bond donor or neutral atom on the ligand is plausible. In BINANA analyses, hydrogen bonds are a common interaction type to identify between residues and ligands, so proposing a hydrogen bond is reasonable given typical protein–ligand contact scenarios.

- Why this is plausible: ASP residues often engage in hydrogen bonding through their carboxylate oxygens or, in some contexts, through their backbone amide groups. If the ligand presents a suitable donor or acceptor, a hydrogen-bonding interaction is a likely labeled event in BINANA’s output for an ASP residue.

- Why there may be hesitation about this being the sole correct answer (conceptual note): Without seeing additional options, it’s hard to compare hydrogen bonding to other plausible interaction types that BINANA might report for an ASP–ligand contact, such as ionic/salt bridge with a positively charged ligand moiety, or a coordinate/metal-mediated interaction if a metal were involved (though ASP is more commonly involved in charge-based or H-bond contacts with organic ligands). If the ligand contains strongly basic or positively charged groups, an ionic interaction (salt bridge) with the ASP carboxylate could also be considered, depending on protonation states.

- If there were other options, a thorough analysis would contrast hydrogen bonding with ionic interactions, hydrophobic contacts, van der Waals contacts, or pi-related interactions, explaining why each would or would not fit the ASP86–ligand contact profile in BINANA’s analysis. In the absence of competing options, the single presented choice remains the focal explanation.

In summary, the provided option Hydrogen bond aligns with common ASP–ligand interaction patterns and with BINANA’s capability to identify hydrogen-bond contacts, making it a reasonable assertion about ASP86’s interaction with the ligand given typical biochemical contexts.

2254 BIOSC 1544 SEC1000 Homework: BINANA

Load the 4EZ3 files Download 4EZ3 files (receptor.pdb and ligand.pdb) into BINANA to answer this and the following questions. What type of interaction does ASP86 form with the ligand?

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