Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3002 |
| PDBID: | 6VGR |
| Chains: | CD_A |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.84 |
| Reference: | 10.1016/j.jsb.2020.107512 |
| Antibody | |
| Antibody: | SC-003 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Tamrintamab(Phase-I) |
| Antigen | |
| Antigen: | Dipeptidase 3 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >6VGR_C|Chain C, E[auth H]|SC-003 Fab Heavy Chain|Homo sapiens (9606) QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYWIEWVRQAPGQGLEWMGEILPGSGNTYYNERFKDRVTITADESTSTAYMELSSLRSEDTAVYYCARRAAAYYSNPEWFAYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: D
Mutation: NULL
| >6VGR_D|Chain D, F[auth L]|SC-003 Fab Light Chain|Homo sapiens (9606) EIVLTQSPATLSLSPGERATLSCTASSSVNSFYLHWYQQKPGLAPRLLIYSTSNLASGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCHQYHRSPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >6VGR_A|Chain A, B|Dipeptidase 3|Homo sapiens (9606) MQPTGREGSRALSRRYLRRLLLLLLLLLLRQPVTRAETTPGAPRALSTLGSPSLFTTPGVPSALTTPGLTTPGTPKTLDLRGRAQALMRSFPLVDGHNDLPQVLRQRYKNVLQDVNLRNFSHGQTSLDRLRDGLVGAQFWSASVSCQSQDQTAVRLALEQIDLIHRMCASYSELELVTSAEGLNSSQKLACLIGVEGGHSLDSSLSVLRSFYVLGVRYLTLTFTCSTPWAESSTKFRHHMYTNVSGLTSFGEKVVEELNRLGMMIDLSYASDTLIRRVLEVSQAPVIFSHSAARAVCDNLLNVPDDILQLLKKNGGIVMVTLSMGVLQCNLLANVSTVADHFDHIRAVIGSEFIGIGGNYDGTGRFPQGLEDVSTYPVLIEELLSRSWSEEELQGVLRGNLLRVFRQVEKVREESRAQSPVEAEFPYGQLSTSCHSHLVPQNGHQATHLEVTKQPTNRVPWRSSNASPYLVPGLVAAATIPTFTQWLC |
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: TRP33 GLU50 TYR59 ARG99 TYR103 TYR104 ASN106 TRP109 D: ILE2 SER27 SER28 ASN30 TYR36 TYR95 HIS96 ARG97 SER98 PRO99 TYR100 A: GLU256 ARG260 GLN283 GLN407 VAL411 GLU413 GLU414 SER415 ARG416 ALA417 GLN418 SER419 PRO420 VAL421 GLU422 |
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)
