Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7268 |
| PDBID: | 7NDF |
| Chains: | D_A |
| Organism: | Vicugna pacos, Escherichia coli |
| Method: | XRD |
| Resolution (Å): | 2.10 |
| Reference: | 10.1126/sciadv.abn6845 |
| Antibody | |
| Antibody: | MsbA#1 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Lipid A ABC transporter ATP-binding protein/permease MsbA |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >7NDF_D|Chain A[auth C], B[auth D]|Nb_MsbA 1|Vicugna pacos (30538) GPSQMQLVESGGGLVQAGGSLRLSCAVSGSIFSIITLAWYRQAPGKPRENVATITRGSRTSYADSVKGRFTISKDNAKSTVYLQMNKLKPEDTADYYCNAEGPAGYWGQGTPVTVS |
Antigen
Chain: A
Mutation: NULL
| >7NDF_A|Chain C[auth A], D[auth B]|Lipid A ABC transporter ATP-binding protein/permease MsbA|Escherichia coli (562) SGDVEFRNVTFTYPGRDVPALRNINLKIPAGKTVALVGRSGSGKSTIASLITRFYDIDEGEILMDGHDLREYTLASLRNQVALVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARMAYAMDFINKMDNGLDTVIGENGVLLSGGQRQRIAIARALLRDSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLSTIEKADEIVVVEDGVIVERGTHNDLLEHRGVYAQLHKMQFGQA |
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)
| D: GLN1 MET2 ILE28 ILE31 ILE32 THR33 ALA35 TYR37 ASN47 THR50 THR52 ARG53 ARG56 SER58 TYR59 ALA60 ASN96 GLU98 GLY99 PRO100 ALA101 GLY102 TYR103 A: ARG360 ASN361 ASN363 GLU547 GLU552 ASP553 VAL555 ILE556 VAL557 GLU558 ARG559 GLY560 ASP564 LEU565 GLU567 HIS568 ARG569 GLY570 VAL571 GLN574 MET578 |
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)
