Dock into the biological assembly, not the asymmetric unit

1HHP, HIV-1 protease. The asymmetric unit holds one of the enzyme's two chains; the pocket is only complete in the dimer.

HIV-1 protease is a homodimer, and its active site lies at the interface: each of the two chains contributes one catalytic aspartate (Asp25). In entry 1HHP the crystal's asymmetric unit contains a single chain, and the second chain is generated by crystal symmetry. A receptor built from the ASU would be half an enzyme with half a pocket.

The ASU tab

1HHP, ASU tab: one chain — **The ASU of 1HHP**: chain A only, 99 residues. Everything in its tree is correct, and it is still not the molecule to dock into.

The Biomol 1 tab

1HHP, Biomol 1 tab: chain A and its symmetry copy — **Biomol 1 of 1HHP**: the dimer. The copy made by the symmetry operation is drawn translucent, and the tree lists chain A only. ADapt opens on Biomol 1 whenever the file defines biological assemblies, so this is what you see first.

The tab you are on when you press receptor PDBQT decides what is written: here, both chains of the dimer. The file records it: REMARK 850 AGFR biomolecule Biomol 1: chains A, 2 copies.

What the copy inherits

The tree shows only the chains of the ASU. A copy made by symmetry follows its original as follows:

Choice made on chain A	Applied to the symmetry copy
Side-chain completion, "include as is"	yes
Mutation	yes
Receptor / ligand checkboxes	no: the copy keeps the default choice
Alternate location	no: the copy keeps the default location

Check the copy. Measured on 1HHP: with A:ASP25 unchecked, the written receptor still contains the copy's ASP25; a mutation of A:ILE50 to ALA is applied in both chains. The alternate-location choice is applied the same way as the checkboxes (as receptor flags on chain A's atoms), so it too stays with chain A. This is ADFR's behaviour, and AGFRgui's. In the written PDBQT the copy also gets a new chain identifier (0 here), because reduce needs unique chain names and ADFR does not rename them back.

When there is no assembly

If a file defines no assembly, or the assembly is the ASU, there is a single tab named ASU or ASU and Biomol 1.

← The tree and the 3D view Choosing between assemblies →