Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6425 |
| PDBID: | 8PE9 |
| Chains: | HL_A |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.15 |
| Reference: | 10.1136/jitc-2023-006720 |
| Antibody | |
| Antibody: | PRTH-101 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Human epithelial discoidin domain-containing receptor 1 |
| Antigen mutation: | No |
| Durg Target: | Q08345 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8PE9_H|Chain B[auth H]|PRTH-101 Fab, heavy chain|Homo sapiens (9606) QVQLVESGGRVVQPGRSLRLSCTASGFSLNRYYMLWVRQAPGKGLEWIGTISYGDTTYYASWAKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARADTGDNGYLGLQLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK |
Light Chain: L
Mutation: NULL
| >8PE9_L|Chain C[auth L]|PRTH-101 Fab, light chain|Homo sapiens (9606) IQMTQSPSSVSASVGDRVTITCQASQSIGSVLAWYQQKPGKAPKLLISGVFDLASGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQYIPYGSSPFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE |
Antigen
Chain: A
Mutation: NULL
| >8PE9_A|Chain A|Epithelial discoidin domain-containing receptor 1|Homo sapiens (9606) RDGLLSYTAPVGQTMYLSEAVYLNDSTYDGHTVGGLQYGGLGQLADGVVGLDDFRKSQELRVWPGYDYVGWSNHSFSSGYVEMEFEFDRLRAFQAMQVHCNNMHTLGARLPGGVECRFRRGPAMAWEGEPMRHNLGGNLGDPRARAVSVPLGGRVARFLQCRFLFAGPWLLFSEISFISDVVN |
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 H: ARG53 TYR54 TYR55 TYR75 THR79 TYR80 ALA120 ASP121 THR122 GLY123 ASP124 ASN125 GLY126 TYR127 LEU128 L: SER50 ILE51 GLY52 SER53 VAL54 VAL73 PHE74 SER89 TYR112 PRO114 TYR115 GLY116 SER117 A: PRO197 VAL198 GLY199 GLN200 THR201 TYR203 LEU204 TYR209 ASN211 VAL220 GLY221 GLY222 LEU223 SER259 HIS261 SER262 PHE263 SER264 SER265 TRP356 |
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)
