Table 3 Summary of the docking results for the CDRs of K9RABVscFv and the antigenic sites on RABV-G.
Docking group | ΔG (kcal/mol) | Kd (M) At 25 °C | scFv | RABV-G | Interaction bond or force | ||||
CDR | sequence | Residue* | Antigenic site | sequence | Residue* | ||||
K9RABVscFv1 VS RABV-G | -12.6 | 6.2 × 10− 10 | CDR2-VH | TSDSGSST | D180 | IIa | KRA | K198 | Electrostatic |
CDR3-VH | AREAYMGLYNFDY | E226 | KRA | K198 | Hydrogen bond | ||||
CDR1-VL | QSLLHSNGNTY | N30 | IIb | GCTNLSGFSY | G34 | Hydrogen bond | |||
CDR1-VL | QSLLHSNGNTY | N30 | GCTNLSGFSY | C35 | Hydrogen bond | ||||
CDR1-VL | QSLLHSNGNTY | N32 | GCTNLSGFSY | C35 | Hydrogen bond | ||||
CDR1-VL | QSLLHSNGNTY | N32 | GCTNLSGFSY | T36 | Hydrogen bond | ||||
CDR1-VH | GFTFSRYK | R158 | GCTNLSGFSY | G40 | Hydrogen bond | ||||
CDR1-VH | GFTFSRYK | R158 | GCTNLSGFSY | S42 | Hydrogen bond | ||||
CDR3-VH | AREAYMGLYNFDY | Y228 | GCTNLSGFSY | G40 | Hydrogen bond | ||||
CDR3-VH | AREAYMGLYNFDY | L231 | GCTNLSGFSY | L38 | Hydrophobic force | ||||
CDR1-VL | QSLLHSNGNTY | Q24 | III | KSVRTWNEI | R333 | Hydrogen bond | |||
CDR3-VL | GQGTHFPWT | H95 | KSVRTWNEI | S331 | Hydrogen bond | ||||
CDR3-VL | GQGTHFPWT | H95 | KSVRTWNEI | R333 | Hydrophobic force | ||||
CDR3-VL | GQGTHFPWT | F96 | KSVRTWNEI | R333 | Hydrogen bond | ||||
CDR3-VL | GQGTHFPWT | P97 | KSVRTWNEI | R333 | Hydrogen bond | ||||
CDR3-VL | GQGTHFPWT | P97 | KSVRTWNEI | E337 | Hydrogen bond | ||||
K9RABVscFv16 VS RABV-G | -11.6 | 2.9 × 10− 9 | CDR1-VH | GFTFSSYH | S158 | IIa | KRA | K198 | Hydrogen bond |
CDR2-VH | IRFDGSYP | D181 | KRA | K198 | Hydrogen bond | ||||
CDR1-VH | GFTFSSYH | T155 | IIb | GCTNLSGFSY | N37 | Hydrogen bond | |||
CDR1-VH | GFTFSSYH | S157 | GCTNLSGFSY | G40 | Hydrogen bond | ||||
CDR1-VH | GFTFSSYH | S158 | GCTNLSGFSY | L38 | Hydrogen bond | ||||
CDR3-VH | ARDVNYYISDY | V227 | GCTNLSGFSY | L38 | Hydrophobic force | ||||
CDR3-VH | ARDVNYYISDY | N228 | GCTNLSGFSY | C35 | Hydrogen bond | ||||
CDR3-VH | ARDVNYYISDY | Y230 | GCTNLSGFSY | T36 | Hydrophobic force | ||||
CDR3-VH | ARDVNYYISDY | Y234 | GCTNLSGFSY | T36 | Hydrogen bond | ||||
CDR1-VL | QSLLHSNGNTY | Q24 | III | KSVRTWNEI | T334 | Hydrogen bond | |||
CDR1-VL | QSLLHSNGNTY | H28 | KSVRTWNEI | S331 | Hydrogen bond | ||||
CDR1-VL | QSLLHSNGNTY | S29 | KSVRTWNEI | S331 | Hydrogen bond | ||||
