Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 371 |
| PDBID: | 2VYR |
| Chains: | H_D |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.00 |
| Reference: | 10.1016/j.jmb.2008.11.043 |
| Antibody | |
| Antibody: | VH9 VH-sdAb |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | human MDM4 N-terminal domain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: H
Mutation: NULL
| >2VYR_H|Chain E, F, G, H, I, J, K, L|HUMAN SINGLE DOMAIN ANTIBODY|HOMO SAPIENS (9606) EVQLLESGGGLVQPGGSLRLSCAASGFTFEEYAMLWVRQAPGKGLEWVSGINARGYTTYYADSVKGRFTISRDNSKNTLYLQMNSLRTEDTAVYYCAKPWYPFMASKGSEFDYWGQGTLVTVSSAAALEIKRASQPELAPEDPEDVEHHHHHH |
Antigen
Chain: D
Mutation: NULL
| >2VYR_D|Chain A, B, C, D|MDM4 PROTEIN|HOMO SAPIENS (9606) ACRISPGQINQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLATATTDA |
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)
| H: VAL2 PHE27 GLU31 TYR32 LYS98 TRP100 TYR101 PRO102 PHE103 MET104 SER106 LYS107 GLU110 PHE111 ASP112 TYR113 TRP114 D: THR48 VAL49 LYS50 GLU51 MET53 HIS54 LEU56 GLY57 GLN58 ILE60 MET61 TYR66 GLN71 HIS72 VAL74 VAL92 LYS93 PRO95 LEU98 TYR99 LEU102 |
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)
