Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4945 |
| PDBID: | 7STZ |
| Chains: | IM_D |
| Organism: | Homo sapiens, Mus musculus |
| Method: | XRD |
| Resolution (Å): | 2.95 |
| Reference: | 10.1093/pnasnexus/pgac163 |
| Antibody | |
| Antibody: | mAb-1_19A11 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Human E-cadherin 1 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7STZ_I|Chain B[auth H], E[auth I]|mAb-1_19A11 Heavy Chain|Mus musculus (10090) MAVLGLLLCLVTFPSCVLSQVQLKESGPGLVAPSQSLSITCTVSGFSLSRYGVHWVRQPPGKGLEWLGMMWGGGNTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTAMYYCASSNYVLGYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDCHHHHHH |
Light Chain: M
Mutation: NULL
| >7STZ_M|Chain C[auth L], F[auth M]|mAb-1_19A11 Light Chain|Mus musculus (10090) MESQTQVLMFLLLWVSGACADIVMTQSPSSLAMSVGQKVTMNCKSSQSLLNSSNQKNYLAWYQQKPGQSPKLLIYFTSTRGSGVPDRFIGSGSGTDFTLTISSVEAEDLADYFCQQHYRTPHTFGGGTKVEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: D
Mutation: NULL
| >7STZ_D|Chain A[auth C], D|Cadherin-1|Homo sapiens (9606) MPLLLLLPLLWAGALADWVIPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTATAVITVTDTNDNPPIFNPTTYKGQVPENEANVVITTLKVTDADAPNTPAWEAVYTILNDDGGQFVVTTNPVNNDGILKTAKGLDFEAKQQYILHVAVTNVVPFEVSLTTSTATVTVDVLDVNEAPIFVPPEKRVEVSEDFGVGQEITSYTAQEPDTFMEQKITYRIWRDTANWLEINPDTGAISTRAELDREDFEHVKNSTYTALIIATDNGSPVATGTGTLLLILSDVNDNAPIPEPRTIFFCERNPKPQVINIIDADLPPNTSPFTAELTHGASANWTIQYNDPTQESIILKPKMALEVGDYKINLKLMDNQNKDQVTTLEVSVCDCEGAAGVCRKASAWSHPQFEKGGGSGGGSGGSAWSHPQFEK |
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)
| Chain residues position delta_SASA
: residuesposition I: SER30 ARG31 TRP52 GLY53 GLY54 GLY55 ASN56 THR57 ASP58 TYR100 GLY103 TYR104 M: ASN31 SER32 SER33 ASN34 TYR38 TYR98 ARG99 THR100 D: ASN12 GLU13 LYS14 GLY15 PRO16 PHE17 PRO18 LYS19 ASN20 PRO47 VAL48 GLY49 ILE52 LYS61 THR63 GLU64 PRO65 LEU66 ASP67 ARG70 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
