Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2147 |
| PDBID: | 6DBG |
| Chains: | C_B |
| Organism: | Listeria monocytogenes, Camelus dromedarius |
| Method: | XRD |
| Resolution (Å): | 1.51 |
| Reference: | 10.1074/jbc.RA118.003888 |
| Antibody | |
| Antibody: | R303 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Listeria virulence factor IInternalin B |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >6DBG_C|Chain C, D|VHH R303|Camelus dromedarius (9838) QVKLEESGGGSVQAGGSLRLSCAASGHTYSTYCMGWFRQVPGKEREGVARINVGGSSTWYADSVRDRFTISQDNAKNTVYLQMNSLKLEDTAIYYCTLHRFCNTWSLGTLNVWGQGTQVTVSSGSEQKLISEEDLNHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >6DBG_B|Chain A, B|Internalin B|Listeria monocytogenes (1639) GAMETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKENLYFQGHHHHHH |
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)
| C: SER30 THR31 ARG50 ASN52 GLY54 GLY55 SER56 SER57 ARG100 PHE101 CYS102 ASN103 THR104 SER106 LEU107 THR109 LEU110 B: GLN80 ILE82 ASN84 LYS102 PHE104 ASN106 TRP124 PHE126 GLU150 SER168 TYR170 ASP189 THR190 SER192 GLU194 GLN211 ASN212 TYR214 ASP233 VAL234 GLU236 PHE238 LYS306 LYS308 |
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)
