Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1597 |
| PDBID: | 5NBD |
| Chains: | C_AB |
| Organism: | Campylobacter jejuni, Lama glama |
| Method: | XRD |
| Resolution (Å): | 3.90 |
| Reference: | 10.1038/srep46641 |
| Antibody | |
| Antibody: | Nb87 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | PglK flippase |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >5NBD_C|Chain C|Nanobody|Lama glama (9844) QVQLQESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAITSGGGSTSYSDAVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAKGYVVDFLDLAEYDSWGQGTQVTVSS |
Antigen
Chain: AB
Mutation: NULL
| >5NBD_A|Chain A, B|WlaB protein|Campylobacter jejuni (197) MVKKLFFILSKEDKNFLFFLLVFSVFVSFIETFAISLVMPFITLASDFSYFDRNKYLISLKEYLNIPVFEIIVYFGVGLIVFYVFRALLNAYYFHLLARFSKGRKHAIAYKVFSKFLNINYEKFTQKNQSEILKSITGEVYNLSTMISSFLLLMSEIFVVLLLYALMLLINYKITLFLSIFMVLNAFILVKILSPIIKKAGLRREEAMKNFFEILNTNLNNFKFIKLKTKEDGVLSLFKAQSEAFSKANITNESVAAVPRIYLEGIGFCVLVFIVVFLVLKNESDISGILSTISIFVLALYRLMPSANRIITSYHDLLYYHSSLNIIYQNLRQEEENLGEGKLSFNQELKICNLSFGYEGKKYLFKNLNLNIKKGEKIAFIGESGCGKSTLVDLIIGLLKPKEGQILIDKQELNASNAKNYRQKIGYIPQNIYLFNDSIAKNITFGDAVDEEKLNKVIKQANLEHFIKNLPQGVQTKVGDGGSNLSGGQKQRIAIARALYLEPEILVLDQATSALDTQSEAKIMDEIYKISKDKTMIIIAHRLSTITQCDKVYRLEHGKLKEEK >5NBD_B|Chain A, B|WlaB protein|Campylobacter jejuni (197) MVKKLFFILSKEDKNFLFFLLVFSVFVSFIETFAISLVMPFITLASDFSYFDRNKYLISLKEYLNIPVFEIIVYFGVGLIVFYVFRALLNAYYFHLLARFSKGRKHAIAYKVFSKFLNINYEKFTQKNQSEILKSITGEVYNLSTMISSFLLLMSEIFVVLLLYALMLLINYKITLFLSIFMVLNAFILVKILSPIIKKAGLRREEAMKNFFEILNTNLNNFKFIKLKTKEDGVLSLFKAQSEAFSKANITNESVAAVPRIYLEGIGFCVLVFIVVFLVLKNESDISGILSTISIFVLALYRLMPSANRIITSYHDLLYYHSSLNIIYQNLRQEEENLGEGKLSFNQELKICNLSFGYEGKKYLFKNLNLNIKKGEKIAFIGESGCGKSTLVDLIIGLLKPKEGQILIDKQELNASNAKNYRQKIGYIPQNIYLFNDSIAKNITFGDAVDEEKLNKVIKQANLEHFIKNLPQGVQTKVGDGGSNLSGGQKQRIAIARALYLEPEILVLDQATSALDTQSEAKIMDEIYKISKDKTMIIIAHRLSTITQCDKVYRLEHGKLKEEK |
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)
| Chain residues position delta_SASA
: residuesposition C: GLN1 GLN3 SER31 TYR32 ALA33 TRP47 ALA50 ILE51 THR52 SER53 SER57 THR58 SER59 TYR60 SER61 LYS98 GLY99 TYR100 VAL101 VAL102 ASP103 PHE104 LEU105 ASP106 ALA108 GLU109 TYR110 SER112 TRP113 A: GLN126 LYS127 LYS209 GLU359 GLY360 LYS361 LYS362 LEU364 B: ASN436 ASN462 HIS465 PHE466 ASN469 LEU470 PRO471 GLN472 THR476 LYS477 GLY479 SER483 ASN484 LEU485 SER486 GLY487 GLY488 GLN489 ARG492 LEU515 ASP516 GLN518 SER519 LYS522 ILE523 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
