Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2926 |
| PDBID: | 6UJC |
| Chains: | EF_B |
| Organism: | Homo sapiens, Mus musculus |
| Method: | EM |
| Resolution (Å): | 3.56 |
| Reference: | 10.1016/j.cell.2019.12.030 |
| Antibody | |
| Antibody: | C6-RGD3 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Integrin β8 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: E
Mutation: NULL
| >6UJC_E|Chain C[auth E]|C6-RGD3 heavy chain Fab|Mus musculus (10090) QIQLVQSGPELKKPGETVKISCKASGYTFTDYSMHWVKQAPGKGLKWVARINTETGEPTFADDFRGRFAVSLETSASTAYLQINNLKNEDTATYFCAIFYYGRDSWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKK |
Light Chain: F
Mutation: NULL
| >6UJC_F|Chain D[auth F]|C6-RGD3 light chain Fab|Mus musculus (10090) DIVMTQSPSSLAVSAGEKVTMSCKSSQSLLGRGDLGRLKKNALAWYQQKPGQSPRLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLLSFGAGTKLELKAADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: B
Mutation: NULL
| >6UJC_B|Chain B|Integrin beta-8|Homo sapiens (9606) EDNRCASSNAASCARCLALGPECGWCVQEDFISGGSRSERCDIVSNLISKGCSVDSIEYPSVHVIIPTENEINTQVTPGEVSIQLRPGAEANFMLKVHPLKKYPVDLYYLVDVSASMHNNIEKLNSVGNDLSRKMAFFSRDFRLGFGSYVDKTVSPYISIHPERIHNQCSDYNLDCMPPHGYIHVLSLTENITEFEKAVHRQKISGNIDTPEGGFDAMLQAAVCESHIGWRKEAKRLLLVMTDQTSHLALDSKLAGIVVPNDGNCHLKNNVYVKSTTMEHPSLGQLSEKLIDNNINVIFAVQGKQFHWYKDLLPLLPGTIAGEIESKAANLNNLVVEAYQKLISEVKVQVENQVQGIYFNITAICPDGSRKPGMEGCRNVTSNDEVLFNVTVTMKKCDVTGGKNYAIIKPIGFNETAKIHIHRNCSCQCEDNRGPKGKCVDETFLDSKCFQCDENKCHFDEDQFSSESCKSHKDQPVCSGRGVCVCGKCSCHKIKLGKVYGKYCEKDDFSCPYHHGNLCAGHGECEAGRCQCFSGWEGDRCQCPSAAAQHCVNSKGQVCSGRGTCVCGRCECTDPRSIGRFCEHCPTCYTACKENWNCMQCLHPHNLSQAILDQCKTSCALMEQQHYVDQTSECFSSPSYLRIFFIIFIVTFLIGLLKVLIIRQVILQWNSNKIKSSSDYRVSASKKDKLILQSVCTRAVTYRREKPEEIKMDISKLNAHETFRCNF |
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)
| E: GLN1 ILE2 GLY26 TYR27 THR28 ASP31 TYR32 SER33 HIS35 ARG50 ASN52 GLU54 THR55 GLU57 PHE99 TYR100 TYR101 GLY102 ARG103 F: GLY31 ARG32 GLY33 ASP34 LEU35 GLY36 LYS40 ALA42 TYR46 TYR59 TRP60 THR63 GLU65 SER66 LYS99 SER101 TYR102 ASN103 LEU105 B: SER114 ALA115 SER116 HIS118 ASN119 ILE121 GLU122 LYS123 ASN125 SER159 ARG164 HIS166 ASN167 CYS169 SER170 ASP171 TYR172 ASN173 LEU174 ASP175 CYS176 PRO178 LYS197 VAL199 HIS200 ARG201 GLN202 LYS203 ILE204 ASN207 ILE208 THR210 GLU212 GLN244 |
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)
