Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7141 |
| PDBID: | 5K59 |
| Chains: | HL_A |
| Organism: | Staphylococcus aureus subsp. aureus USA300, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.84 |
| Reference: | 10.1080/19420862.2016.1215791 |
| Antibody | |
| Antibody: | 5K59 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Berlimatoxumab(Phase-II) |
| Antigen | |
| Antigen: | Leukocidin-like protein 1 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >5K59_H|Chain E, G[auth H]|Fab heavy chain|Homo sapiens (9606) ELQLQESGPGLVKPSETLSLTCTVSGGSISSGSYYWDWIRQPPGKGLEWIGNIYKSGSTYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARERGMHYMDVWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT |
Light Chain: L
Mutation: NULL
| >5K59_L|Chain F, H[auth L]|Fab light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQSINSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQQFDPPFTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >5K59_A|Chain B[auth A], D[auth B]|Uncharacterized leukocidin-like protein 1|Staphylococcus aureus (strain USA300) (367830) SLKINSEIKQVSEKNLDGDTKMYTRTATTSDSQKNITQSLQFNFLTEPNYDKETVFIKAKGTIGSGLRILDPNGYWNSTLRWPGSYSVSIQNVDDNNNTNVTDFAPKNQDESREVKYTYGYKTGGDFSINRGGLTGNITKESNYSETISYQQPSYRTLLDQSTSHKGVGWKVEAHLINNMGHDHTRQLTNDSDNRTKSEIFSLTRNGNLWAKDNFTPKDKMPVTVSEGFNPEFLAVMSHDKKDKGKSQFVVHYKRSMDEFKIDWNRHGFWGYWSGENHVDKKEEKLSALYEVDWKTHNVKFVKVLNDNEKK |
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: SER33 TYR35 TRP49 ASN52 TYR54 SER56 SER58 THR59 TYR60 GLU100 ARG101 GLY102 MET103 HIS104 L: ASN30 SER31 TYR32 TYR49 ALA50 GLN91 PHE92 PRO94 PHE96 A: PRO70 ASN71 TYR73 TRP74 LEU201 ASN206 LEU207 TRP208 LYS210 ASP211 TRP262 ARG264 GLY266 PHE267 TRP271 |
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)
