Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2378 |
| PDBID: | 6K0Y |
| Chains: | AB_C |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 1.70 |
| Reference: | 10.1038/s41598-019-54231-w |
| Antibody | |
| Antibody: | 059c Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Programmed cell death protein 1 (PD-1) |
| Antigen mutation: | No |
| Durg Target: | Q15116 |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >6K0Y_A|Chain A|Antibody Heavy Chain|Homo sapiens (9606) QVQLQESGPGLVKPSETLSLTCAVSGHSIRGSYFWGWIRQPPGRGLEWIGSIYHSGSTYTNPSLKSRATISVDTSKNQFSLKLNSVTAADTAVYYCARDLDIATTRDYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE |
Light Chain: B
Mutation: NULL
| >6K0Y_B|Chain B|Antibody Light Chain|Homo sapiens (9606) DIQLTQSPSFLSASVGDRVTIICRASQGINNYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQLDSYPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: NULL
| >6K0Y_C|Chain C|Programmed cell death protein 1|Homo sapiens (9606) LDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAEVPTAHPSPSPRPAGQFQ |
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 A: HIS27 GLY31 SER32 TYR33 PHE34 TYR53 SER55 SER57 TYR59 ASP101 ILE102 ALA103 B: GLN27 GLY28 TYR32 LEU91 ASP92 SER93 TYR94 ARG96 C: SER60 GLU61 SER62 PHE63 VAL64 LYS78 PRO83 ASP85 ARG86 ILE126 LEU128 ALA129 PRO130 LYS131 ALA132 GLN133 ILE134 |
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)
