Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 563 |
| PDBID: | 3KJ4 |
| Chains: | HL_A |
| Organism: | Mus musculus, Rattus norvegicus |
| Method: | XRD |
| Resolution (Å): | 3.10 |
| Reference: | 10.1042/BA20100061 |
| Antibody | |
| Antibody: | 1D9 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Reticulon-4 receptor |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >3KJ4_H|Chain B[auth C], E[auth H]|Fab fragment 1D9 heavy chain|Mus musculus (10090) QVQLKESGPGLVAPSQSLSISCSVSGFSLSSYGVHWVRQSPGQGLEWLGVIWSGGNTHYNSALMSRLSISKENSKNQVFLKMNSLQTDDTAIYYCARVGIYYEGAWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR |
Light Chain: L
Mutation: NULL
| >3KJ4_L|Chain A[auth B], D[auth L]|Fab fragment 1D9 light chain|Mus musculus (10090) DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRNRKNYLAWYQQKPGQSPKPLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCMQSYNLFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC |
Antigen
Chain: A
Mutation: NULL
| >3KJ4_A|Chain C[auth A], F[auth D]|Reticulon-4 receptor|Rattus norvegicus (10116) CPGACVCYNEPKVTTSCPQQGLQAVPTGIPASSQRIFLHGNRISYVPAASFQSCRNLTILWLHSNALAGIDAAAFTGLTLLEQLDLSDNAQLRVVDPTTFRGLGHLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNNLQALPDNTFRDLGNLTHLFLHGNRIPSVPEHAFRGLHSLDRLLLHQNHVARVHPHAFRDLGRLMTLYLFANNLSMLPAEVLVPLRSLQYLRLNDNPWVCDCRARPLWAWLQKFRGSSSEVPCNLPQRLAGRDLKRLAASDLEGCAVA |
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)
| L: ASN31 ARG33 ASN34 LYS36 TYR38 TRP56 H: SER30 SER31 TYR32 TRP52 SER53 GLY54 GLY55 ASN56 VAL98 GLY99 ILE100 TYR101 TYR102 GLU103 GLY104 A: CYS27 PRO28 LEU48 GLN49 ALA50 VAL51 PRO52 THR53 GLY54 ILE55 PRO56 ALA57 SER58 SER70 TYR71 PRO73 ALA74 ALA75 SER76 GLN78 SER79 ARG81 ALA94 GLY95 GLN117 LEU118 ARG119 VAL120 |
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)
