Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3253 |
| PDBID: | 6Y90 |
| Chains: | CD_B |
| Organism: | Homo sapiens, Mus musculus |
| Method: | EM |
| Resolution (Å): | 3.69 |
| Reference: | 10.1126/science.abb8008 |
| Antibody | |
| Antibody: | Rituximab Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Eramkafusp(Phase-I); Ripertamab(Phase-III); Rituximab(Approved); |
| Antigen | |
| Antigen: | B-lymphocyte antigen CD20 |
| Antigen mutation: | No |
| Durg Target: | P11836 |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >6Y90_C|Chain C, E[auth H]|Rituximab Fab Heavy Chain|Mus musculus (10090) QVQLQQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGRGLEWIGAIYPGNGDTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYYCARSTYYGGDWYFNVWGAGTTVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: D
Mutation: NULL
| >6Y90_D|Chain D, F[auth L]|Rituximab Fab Light Chain|Mus musculus (10090) QIVLSQSPAILSASPGEKVTMTCRASSSVSYIHWFQQKPGSSPKPWIYATSNLASGVPVRFSGSGSGTSYSLTISRVEAEDAATYYCQQWTSNPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: B
Mutation: NULL
| >6Y90_B|Chain A, B|B-lymphocyte antigen CD20|Homo sapiens (9606) FMRESKTLGAVQIMNGLFHIALGGLLMIPAGIYAPICVTVWYPLWGGIMYIISGSLLAATEKNSRKCLVKGKMIMNSLSLFAAISGMILSIMDILNIKISHFLKMESLNFIRAHTPYINIYNCEPANPSEKNSPSTQYCYSIQSLFLGILSVMLIFAFFQELVIAGIVENEW |
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: SER31 ASN33 HIS35 TRP47 ALA50 ILE51 TYR52 ASN55 ASP57 THR58 SER59 TYR60 GLN62 SER99 TYR101 TRP106 D: GLN1 ILE2 SER26 SER27 SER28 VAL29 SER30 GLY67 THR68 TRP90 THR91 SER92 ASN93 PRO94 PRO95 B: ILE76 TYR77 SER144 HIS145 LYS148 GLU150 ARG156 PRO160 TYR161 ILE162 ASN163 ASN166 CYS167 GLU168 PRO169 ALA170 ASN171 PRO172 SER173 GLU174 LYS175 ASN176 |
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)
