Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5134 |
| PDBID: | 7UBX |
| Chains: | C_B |
| Organism: | Clostridioides difficile, Camelidae |
| Method: | XRD |
| Resolution (Å): | 1.81 |
| Reference: | 10.3389/fimmu.2022.978858 |
| Antibody | |
| Antibody: | AA6 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Clostridium difficile toxin A |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >7UBX_C|Chain B[auth C], D|Nanobody VHH AA6|Camelidae (9835) SQVQLVESGGGLVQPGGSLRLSCAASGFTFSDYVMTWVRQAPGKGPEWIATINTDGSTMRDDSTKGRFTISRDNAKNTLYLQMTSLKPEDTALYYCARGRVISASAIRGAVRGPGTQVTVSS |
Antigen
Chain: B
Mutation: NULL
| >7UBX_B|Chain A, C[auth B]|Toxin A|Clostridioides difficile (1496) SMSLSIAATVASIVGIGAEVTIFLLPIAGISAGIPSLVNNELILHDKATSVVNYFNHLSESKKYGPLKTEDDKILVPIDDLVISEIDFNNNSIKLGTCNILAMEGGSGHTVTGNIDHFFSSPSISSHIPSLSIYSAIGIETENLDFSKKIMMLPNAPSRVFWWETGAVPGLRSLENDGTRLLDSIRDLYPGKFYWRFYAFFDYAITTLKPVYEDTNIKIKLDKDTRNFIMPTITTNEIRNKLSYSFDGAGGTYSLLLSSYPISTNINLSKDDLWIFNIDNEVREISIENGTIKKGKLIKDVLSKIDINKNKLIIGNQTIDFSGDIDNKDRYIFLTCELDDKISLIIEINLVAKSYSLLLSGDKNYLISNLSNTIEKINTLGLDSKNIAYNYTD |
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: ASP31 TYR32 VAL33 ARG38 GLU46 TRP47 ASN52 THR53 ASP54 SER56 THR57 MET58 ARG59 ASP60 ASP61 SER62 ARG66 LYS86 GLU88 ASP89 ARG97 GLY98 ARG99 ILE101 SER102 SER104 ALA105 B: ILE1098 ILE1105 PRO1106 SER1107 LEU1108 ASN1110 ASN1111 LEU1113 THR1305 THR1306 ASN1307 GLU1308 ARG1310 SER1330 TYR1331 PRO1332 GLU1352 ARG1354 GLU1355 ILE1356 SER1357 ILE1358 LYS1364 LYS1367 ILE1369 LYS1370 ASP1371 VAL1372 ILE1384 GLY1386 ASN1387 THR1389 |
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)
