Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1438 |
| PDBID: | 5IMK |
| Chains: | B_A |
| Organism: | Camelidae, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 1.23 |
| Reference: | 10.1016/j.imbio.2016.11.008 |
| Antibody | |
| Antibody: | Nb119 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | human Vsig4 in Spacegroup C2 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >5IMK_B|Chain A[auth B]|Nanobody|Camelidae (9835) QVQLVESGGGLVQAGGSLRLSCAASGRTFSSYGMGWFRQAPGKEREFVAAIRWNGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAGRWDKYGSSFQDEYDYWGQGTQVTVSSHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >5IMK_A|Chain B[auth A]|V-set and immunoglobulin domain-containing protein 4|Homo sapiens (9606) HHHHHHGRPILEVPESVTGPWKGDVNLPCTYDPLQGYTQVLVKWLVQRGSDPVTIFLRDSSGDHIQQAKYQGRLHVSHKVPGDVSLQLSTLEMDDRSHYTCEVTWQTPDGNQVVRDKITELRVQKLSVSKPTVTTGSGYGFTVPQGMRISLQCQARGSPPISYIWYKQQTNNQEPIKVATLSTLLFKPAVIADSGSYFCTAKGQVGSEQHSDIVKFVVKD |
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)
| B: THR27 SER30 TYR31 ARG51 TRP52 ASN53 ARG99 TRP100 ASP101 LYS102 TYR103 GLY104 PHE107 ASP109 GLU110 ASP112 TYR113 A: ARG1 PRO2 ILE3 LEU4 VAL6 GLU8 LYS36 LEU38 GLN40 GLY42 SER43 ASP44 PRO45 HIS91 THR93 GLU95 VAL107 ARG108 ASP109 LYS110 ILE111 GLU113 |
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)
