Load the 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 (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

The question asks: What type of interaction does ASP86 form with the ligand?

Option analysis:
- The provided answer is: Hydrogen bond.
  This implies that, according to BINANA’s analysis of the receptor-ligand complex, the ASP86 residue participates in a hydrogen-bond interaction with the ligand. In typical protein–ligand contacts, aspartate (ASP) side chains contain a carboxylate group that can serve as a hydrogen-bond acceptor (and, in some contexts, may participate in donor interactions if a proton is on a nearby donor group). If the ligand has an appropriate hydrogen-bond donor or acceptor geometry and orientation, a hydrogen bond can be established between ASP86 and the ligand. The classification as a hydrogen bond is consistent with common types of noncovalent interactions observed in docking and structural analyses.

Notes on potential misconceptions:
- If one expected a purely ionic or salt-bridge interaction, that would emphasize charge–charge attraction rather than a directional hydrogen-bond pattern. In many cases, a carboxylate group acts primarily as an H-bond acceptor rather than a strong donor, so the interaction may be best described as a hydrogen bond where ASP86 is the acceptor and the ligand provides the hydrogen donor.
- If the ligand lacked compatible donors/acceptors or if geometry was highly distorted, one might question the presence of a hydrogen bond. In BINANA’s output, however, the designated interaction type would still be reported as a hydrogen bond if the criteria for H-bond geometry (distance and angle) are met.

Contextual considerations:
- The question specifically references loading the 4EZ3 files and analyzing interactions in BINANA. Within BINANA’s framework, hydrogen bonds are among the primary interaction types reported between receptor residues (like ASP86) and ligand atoms.
- Because the provided options list only a single choice, there is no alternative option to evaluate for potential misunderstandings (e.g., hydrophobic contact, salt bridge, or van der Waals interaction). If such options existed, one would assess compatibility with residue chemistry and ligand functional groups to decide.

Summary takeaway:
- The interaction type identified for ASP86 with the ligand is a hydrogen bond, reflecting a directional, non-covalent interaction consistent with ASP86 acting as an H-bond acceptor (or, less commonly, donor) in the receptor-ligand interface based on BINANA’s analysis.

2254 BIOSC 1544 SEC1000 Homework: BINANA

Load the 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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