TABLE 2.
Residues and domains of the RdRp of the viruses that formed contact interface with the residues in CDRs of the HuscFv34.
| HCV RdRp |
HuscFv34 |
Interactive bond | ||
| Residue | Region | Residue | Region | |
| A25 | Finger | V167 | VL-CDR1 | Alkyl |
| N28 | Finger | Q164 | VL-CDR1 | Hydrogen |
| N28 | Finger | G165 | VL-CDR1 | Hydrogen |
| S29 | Finger | H168 | VL-CDR1 | Hydrogen |
| S29 | Finger | H169 | VL-CDR1 | Hydrogen |
| R32 | Finger | Q235 | VL-CDR3 | Hydrogen |
| R32 | Finger | S137 | VH-CDR3 | Hydrogen |
| R32 | Finger | P237 | VL-CDR3 | Hydrogen |
| R32 | Finger | N138 | VH-CDR3 | Hydrogen |
| S431 | Thumb | H169 | VL-CDR1 | Hydrogen |
| R490 | Thumb | Q62 | VH-CDR2 | Hydrogen |
| R498 | Thumb | N57 | VH-CDR2 | Hydrogen |
| R498 | Thumb | T58 | VH-CDR2 | Hydrogen |
| V499 | Thumb | F236 | VL-CDR3 | Pi-Alkyl |
| H502 | Thumb | D33 | VH-CDR1 | Hydrogen |
| H502 | Thumb | W50 | VH-CDR2 | Pi-Pi |
| R503 | Thumb | D103 | VH-CDR3 | Hydrogen |
| R503 | Thumb | H169 | VL-CDR1 | Pi-Alkyl |
| R503 | Thumb | T234 | VL-CDR3 | Hydrogen |
| K531 | Thumb | N54 | VH-CDR2 | Hydrogen |
|
| ||||
|
DENV1 RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| H800* | Thumb | G165 | VL-CDR1 | Hydrogen |
| T805* | Thumb | F236 | VL-CDR3 | Pi-Sigma |
| E806* | Thumb | Q164 | VL-CDR1 | Hydrogen |
| D807* | Thumb | H169 | VL-CDR1 | Hydrogen |
| D807* | Thumb | H168 | VL-CDR1 | Hydrogen |
| L809* | Thumb | H169 | VL-CDR1 | Hydrogen |
| S810 | Thumb | V167 | VL-CDR1 | Hydrogen |
| S810 | Thumb | H169 | VL-CDR1 | Hydrogen |
| S810 | Thumb | H168 | VL-CDR1 | Hydrogen |
| R814 | Thumb | G165 | VL-CDR1 | Hydrogen |
| V829 | Thumb | H169 | VL-CDR1 | Pi-Anion |
| S830 | Thumb | H169 | VL-CDR1 | Pi-Anion |
| S892 | Thumb | N54 | VH-CDR2 | Electrostatic |
| D893 | Thumb | S55 | VH-CDR2 | Electrostatic |
| L898 | Thumb | D103 | VH-CDR3 | Hydrogen |
| W899 | Thumb | D103 | VH-CDR3 | Hydrogen |
|
| ||||
|
DENV2 RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| K719 | Thumb | Q235 | VL-CDR3 | Hydrogen |
| R770 | Thumb | H169 | VL-CDR1 | Hydrogen |
| E834 | Thumb | H168 | VL-CDR1 | Salt bridge, Electrostatic |
| E834 | Thumb | H169 | VL-CDR1 | Hydrogen |
| E834 | Thumb | R238 | VL-CDR3 | Electrostatic |
| Y838 | Thumb | H169 | VL-CDR1 | Electrostatic |
| R856 | Thumb | H169 | VL-CDR1 | Hydrogen |
| R856 | Thumb | Y102 | VH-CDR3 | Pi-Alkyl |
| A860 | Thumb | Y102 | VH-CDR3 | Hydrogen |
| K861 | Thumb | G105 | VH-CDR3 | Hydrogen |
| K861 | Thumb | D106 | VH-CDR3 | Salt bridge, Electrostatic |
| N868 | Thumb | N54 | VH-CDR2 | Hydrogen |
| D881 | Thumb | N54 | VH-CDR2 | Hydrogen |
| D881 | Thumb | S55 | VH-CDR2 | Hydrogen |
| D881 | Thumb | N57 | VH-CDR2 | Hydrogen |
|
| ||||
|
DENV3 RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| T806* | Thumb | H169 | VL-CDR1 | Hydrogen |
| E807* | Thumb | H169 | VL-CDR1 | Hydrogen |
| D808* | Thumb | H169 | VL-CDR1 | Hydrogen, Electrostatic |
| D808* | Thumb | Y102 | VH-CDR3 | Hydrogen |
| T832 | Thumb | Y104 | VH-CDR3 | Hydrogen |
| W833 | Thumb | Y104 | VH-CDR3 | Hydrogen |
| E834 | Thumb | Y104 | VH-CDR3 | Hydrogen, Pi-Anion |
| E834 | Thumb | S31 | VH-CDR1 | Hydrogen |
| E834 | Thumb | H32 | VH-CDR1 | Electrostatic, Hydrogen |
| A860 | Thumb | S55 | VH-CDR2 | Hydrogen |
| Q861 | Thumb | R72 | VH-CDR2 | Hydrogen |
| L864 | Thumb | N57 | VH-CDR2 | Hydrogen |
| E878 | Thumb | Q164 | VL-CDR1 | Hydrogen |
| E878 | Thumb | Q235 | VL-CDR3 | Hydrogen |
| L880 | Thumb | H168 | VL-CDR1 | Pi-Sigma |
| D881 | Thumb | F236 | VL-CDR3 | Pi-Anion, Pi-Sigma |
| Y882 | Thumb | H169 | VL-CDR1 | Hydrogen |
| M883 | Thumb | N52 | VH-CDR2 | Hydrogen |
|
| ||||
|
DENV4 RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| K812 | Thumb | D106 | VH-CDR3 | Hydrogen, Electrostatic |
| K812 | Thumb | E108 | VH-CDR3 | Hydrogen, Electrostatic |
| P830 | Thumb | T28 | VH-CDR1 | Hydrogen |
| H832 | Thumb | H32 | VH-CDR1 | Hydrogen |
| H832 | Thumb | G26 | Electrostatic | |
| H832 | Thumb | T28 | VH-CDR1 | Hydrogen, Electrostatic |
| E835 | Thumb | Y104 | VH-CDR3 | Hydrogen |
| D836 | Thumb | T30 | VH-CDR1 | Hydrogen |
| R872 | Thumb | N170 | VL-CDR1 | Hydrogen |
| Y880 | Thumb | N172 | VL-CDR1 | Hydrogen |
| D882 | Thumb | N172 | VL-CDR1 | Hydrogen |
| P885 | Thumb | Y102 | VH-CDR3 | Pi-Alkyl |
| R888 | Thumb | N52 | VH-CDR2 | Hydrogen |
| E895 | Thumb | H168 | VL-CDR1 | Hydrogen |
| E895 | Thumb | Q235 | VL-CDR3 | Hydrogen |
| E895 | Thumb | F236 | VL-CDR3 | Hydrogen |
| Y890 | Thumb | Y102 | VH-CDR3 | Hydrogen |
| A892 | Thumb | Y102 | VH-CDR3 | Pi-Alkyl |
|
| ||||
|
ZIKV RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| K721 | Thumb | H169 | VL-CDR1 | Hydrogen |
| L776 | Thumb | G171 | VL-CDR1 | Hydrogen |
| K843 | Thumb | N170 | VL-CDR1 | Pi-Cation |
| K843 | Thumb | Q192 | VL-CDR2 | Hydrogen |
| G854 | Thumb | Y174 | VL-CDR1 | Hydrogen |
| A862 | Thumb | Y102 | VH-CDR3 | Hydrogen |
| A862, E863 | Thumb | Y102 | VH-CDR3 | Pi-Alkyl |
| E863 | Thumb | F236 | VL-CDR3 | Hydrogen |
| E863 | Thumb | V167 | VL-CDR1 | Pi-Alkyl |
| E863 | Thumb | S137 | VH-CDR3 | Hydrogen |
| I865 | Thumb | D103 | VH-CDR3 | Amide-Pi Stacked |
| K866 | Thumb | D103 | VH-CDR3 | Hydrogen, Alkyl |
| K866 | Thumb | Y104 | VH-CDR3 | Hydrogen, Pi-Alkyl |
| K866 | Thumb | G105 | VH-CDR3 | Hydrogen |
| K866 | Thumb | Y107 | VH-CDR3 | Hydrogen |
| K866 | Thumb | D33 | VH-CDR1 | Hydrogen |
| D884 | Thumb | S55 | VH-CDR2 | Salt bridge, Electrostatic |
| D884 | Thumb | N57 | VH-CDR2 | Electrostatic |
|
| ||||
|
JEV RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| K724 | Thumb | Q235 | VL-CDR3 | Hydrogen |
| K724 | Thumb | G165 | VL-CDR1 | Hydrogen |
| K724 | Thumb | V167 | VL-CDR1 | Hydrogen |
| R775 | Thumb | N170 | VL-CDR1 | Hydrogen |
| T839 | Thumb | H168 | VL-CDR1 | Hydrogen |
| T839 | Thumb | H169 | VL-CDR1 | Hydrogen |
| D840 | Thumb | H169 | VL-CDR1 | Hydrogen |
| Y843 | Thumb | H169 | VL-CDR1 | Hydrogen |
| K846 | Thumb | N170 | VL-CDR1 | Hydrogen |
| K846 | Thumb | G171 | VL-CDR1 | Hydrogen |
| Y869 | Thumb | Y104 | VH-CDR3 | Hydrogen |
| R876 | Thumb | N54 | VH-CDR2 | Hydrogen |
| D886 | Thumb | N54 | VH-CDR2 | Hydrogen |
| T889 | Thumb | N57 | VH-CDR2 | Hydrogen |
| T889 | Thumb | D103 | VH-CDR3 | Hydrogen |
| T889 | Thumb | D33 | VH-CDR1 | Hydrogen |
|
| ||||
|
EV71 RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| K427 | Thumb | F236 | VL-CDR3 | Hydrogen |
| Q428 | Thumb | Q164 | VL-CDR1 | Hydrogen |
| Q428 | Thumb | G165 | VL-CDR1 | Hydrogen |
| Q428 | Thumb | V167 | VL-CDR1 | Hydrogen |
| E431 | Thumb | F236 | VL-CDR3 | Hydrogen |
| S435 | Thumb | H168 | VL-CDR1 | Hydrogen |
| T436 | Thumb | H169 | VL-CDR1 | Hydrogen |
| R438 | Thumb | T58 | VH-CDR2 | Hydrogen |
| R444 | Thumb | Y104 | VH-CDR3 | Pi-Cation |
| R444 | Thumb | D33 | VH-CDR1 | Electrostatic |
| R444 | Thumb | N57 | VH-CDR2 | Hydrogen |
| R444 | Thumb | D103 | VH-CDR3 | Hydrogen, Electrostatic |
| L446 | Thumb | N57 | VH-CDR2 | Hydrogen |
|
| ||||
|
CVA16 RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| H383 | Thumb | N57 | VH-CDR2 | Pi-Sigma |
| H383 | Thumb | T58 | VH-CDR2 | Hydrogen |
| H383 | Thumb | G59 | VH-CDR2 | Hydrogen |
| Q384 | Thumb | N54 | VH-CDR2 | Hydrogen |
| K427 | Thumb | D33 | VH-CDR1 | Electrostatic |
| K427 | Thumb | F236 | VL-CDR3 | Pi-Anion |
| E428 | Thumb | P237 | VL-CDR3 | Hydrogen |
| E428 | Thumb | Y102 | VH-CDR3 | Hydrogen |
| E428 | Thumb | R238 | VL-CDR3 | Electrostatic |
| E431 | Thumb | H169 | VL-CDR1 | Salt bridge, Electrostatic |
| E431 | Thumb | H169 | VL-CDR1 | Pi-Alkyl |
| K432 | Thumb | Q164 | VL-CDR1 | Hydrogen |
| V434 | Thumb | H169 | VL-CDR1 | Hydrogen |
| S435 | Thumb | F236 | VL-CDR3 | Pi-Alkyl |
| R438 | Thumb | H169 | VL-CDR1 | Hydrogen |
| R438 | Thumb | H168 | VL-CDR1 | Salt bridge, Electrostatic |
| N450 | Thumb | D103 | VH-CDR3 | Salt bridge, Electrostatic |
| N450 | Thumb | Q235 | VL-CDR3 | Hydrogen |
|
| ||||
|
PEDV RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| K412 | Fingers | H169 | VL-CDR1 | Hydrogen |
| E413 | Fingers | H169 | VL-CDR1 | Electrostatic, Hydrogen |
| E413 | Fingers | Y102 | VH-CDR3 | Hydrogen |
|
| ||||
|
PEDV RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| E420 | Fingers | H169 | VL-CDR1 | Electrostatic, Hydrogen |
| E420 | Fingers | Q235 | VL-CDR3 | Hydrogen |
| E420 | Fingers | H168 | VL-CDR1 | Salt bridge, Electrostatic, Hydrogen |
| H885 | Thumb | D103 | VH-CDR3 | Pi-Anion, Hydrogen |
| K888 | Thumb | D103 | VH-CDR3 | Salt bridge, Electrostatic |
| K888 | Thumb | D33 | VH-CDR1 | Electrostatic |
| K888 | Thumb | W50 | Pi-Cation | |
| K888 | Thumb | Y104 | VH-CDR3 | Pi-Alkyl |
| N891 | Thumb | Y104 | VH-CDR3 | Hydrogen |
| A892 | Thumb | Y104 | VH-CDR3 | Pi-Alkyl |
| E896 | Thumb | D106 | VH-CDR3 | Hydrogen |
| E896 | Thumb | H32 | VH-CDR1 | Electrostatic |
|
| ||||
|
SARS-CoV-2 RdRp
|
HuscFv34
|
Interactive bond | ||
| Residue | Region | Residue | Region | |
|
| ||||
| F415 | Fingers | N54 | VH-CDR2 | Hydrogen |
| N416 | Fingers | S55 | VH-CDR2 | Hydrogen |
| D418 | Fingers | S55 | VH-CDR2 | Hydrogen |
| D418 | Fingers | N52 | VH-CDR2 | Hydrogen |
| D418 | Fingers | Y104 | VH-CDR3 | Hydrogen |
| K426 | Fingers | Y102 | VH-CDR3 | Hydrogen |
| K849 | Thumb | S55 | VH-CDR2 | Hydrogen |
| Q886 | Thumb | H169 | VL-CDR1 | Hydrogen |
| R889 | Thumb | H169 | VL-CDR1 | Hydrogen, Pi-Alkyl |
| K890 | Thumb | D103 | VH-CDR3 | Salt bridge, Electrostatic |
| K890 | Thumb | H169 | VL-CDR1 | Pi-Alkyl |
| D893 | Thumb | H168 | VL-CDR1 | Salt bridge, Electrostatic |
| E894 | Thumb | N57 | VH-CDR2 | Hydrogen |
| E894 | Thumb | F236 | VL-CDR3 | Pi-Sigma |
*Priming loop of the thumb domain.