Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7498 |
| PDBID: | 6V7Y |
| Chains: | F_A |
| Organism: | Homo sapiens, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1038/s43018-020-00111-6 |
| Antibody | |
| Antibody: | ID5 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Antigen-presenting glycoprotein CD1d |
| Antigen mutation: | No |
| Durg Target: | P15813; P05412; |
Sequence information
Antibody
Chain: F
Mutation: NULL
| >6V7Y_F|Chain C[auth F]|Nanobody VHH ID5|Lama glama (9844) EVQLVESGGGLVQAGGSLRLSCAASGSSFSSYTMGWFRQAPGKEREIVAGIRWSDESPIYADSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAARLVPPGIPIPRTSESMRYWGKGTLVTVSS |
Antigen
Chain: A
Mutation: NULL
| >6V7Y_A|Chain A|Antigen-presenting glycoprotein CD1d|Homo sapiens (9606) MQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGSLVPRGSGSRIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHGSGLNDIFEAQKIEWHEHHHHHH |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| F: SER27 SER28 SER30 SER31 TYR32 TRP53 SER54 ASP55 ASN74 ARG99 LEU100 VAL101 PRO102 PRO103 GLY104 ILE105 PRO108 GLU112 SER113 MET114 ARG115 TRP117 A: PHE55 SER56 GLN58 GLN59 GLU61 THR62 LEU63 HIS65 ILE66 VAL69 TRP150 GLU153 THR154 TRP157 LEU158 GLY161 THR162 GLN165 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
