Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5617 |
| PDBID: | 7XNF |
| Chains: | HL_A |
| Organism: | Homo sapiens, Pangolin coronavirus |
| Method: | XRD |
| Resolution (Å): | 2.79 |
| Reference: | 10.1016/j.celrep.2022.111831 |
| Antibody | |
| Antibody: | P2C-1F11 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Amubarvimab(Phase-II/III) |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein GX/P2V/2017 RBD |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7XNF_H|Chain A[auth H]|P2C-1F11 Heavy Chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCAASGITVSSNYMNWVRQAPGKGLEWVSLIYSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYHCARDLVVYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCP |
Light Chain: L
Mutation: NULL
| >7XNF_L|Chain B[auth L]|P2C-1F11 Lambda chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS |
Antigen
Chain: A
Mutation: NULL
| >7XNF_A|Chain C[auth A]|Spike protein S1|Pangolin coronavirus (2708335) RVQPTISIVRFPNITNLCPFGEVFNASKFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLNDLCFTNVYADSFVVKGDEVRQIAPGQTGVIADYNYKLPDDFTGCVIAWNSVKQDALTGGNYGYLYRLFRKSKLKPFERDISTEIYQAGSTPCNGQVGLNCYYPLERYGFHPTTGVNYQPFRVVVLSFELLNGPATVCGPHHHHHH |
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: GLU1 VAL2 GLY26 ILE27 THR28 SER30 SER31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 TYR58 ARG97 LEU99 VAL100 VAL101 TYR102 L: SER28 VAL29 SER30 TYR33 A: LYS403 GLU406 THR415 GLY416 VAL417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 LYS460 TYR473 GLN474 ALA475 GLY476 SER477 LEU486 ASN487 TYR489 TYR490 GLU493 GLY502 TYR505 |
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)
