FIG 4.
Conformational change in 13D4 HCDR3 and HA, with HCDR3 adapting to fit into the RBS. (A) The free 13D4 and unbound HA monomer (from PDB accession no. 2IBX) were superimposed on corresponding components of the 13D4:HAhr complex. Fabs are depicted in cartoon mode, with free Fab in yellow and bound Fab in forest green. HA molecules are shown in surface presentation, with unbound HA in white and bound HA in salmon. (B) Enlarged view of the HCDR3 rearrangement (boxed in panel A). For clarity, other parts of the interaction from panel A have been omitted. Hydrogen bonds are shown as black dashed lines. W100dH and E100aH in the free Fab are shown in transparent sphere dot representation, demonstrating clashing with the 220 loop. (C) Conformational changes to HA while binding with 13D4. For clarity, other parts of the interaction from panel A are omitted. (D) Eventual fine fitting of HCDR3 to the RBS. The non-H atoms of HCDR3 up to 4.5 Å from HA are shown in dot sphere representation.