Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5212 |
| PDBID: | 7URQ |
| Chains: | HL_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.05 |
| Reference: | 10.3389/fimmu.2023.1178355 |
| Antibody | |
| Antibody: | CoV11 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 S delta variant spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7URQ_H|Chain B[auth H]|COV11 Fab HEAVY CHAIN|Homo sapiens (9606) EVQLVESGGGLIQPGGSLRLSCAASGFIVSRNYMIWVRQAPGKGLEWVSVIYSGGSTFYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDLEVAGAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >7URQ_L|Chain C[auth L]|COV11 Fab LIGHT CHAIN|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATLSCRASQSISSSYLAWYQQKPGQAPRLLIYGATSRATGTPDRFSGSGSGTDFTLTINRLEPEDFAVYYCQQYGSSPGYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSRDSTYSLGSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: L136R/T162K
| >7URQ_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) GSRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKLEHHHHHH |
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 PHE27 ILE28 SER30 ARG31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 PHE58 ARG94 LEU96 GLU97 VAL98 ALA99 ASP101 TYR102 L: SER28 ILE29 SER30 SER31 SER32 TYR33 SER68 GLY69 GLY93 SER94 SER95 TYR98 A: ARG403 ASP405 ARG408 THR415 GLY416 LYS417 ASP420 TYR421 TYR449 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 SER477 LYS478 PHE486 ASN487 TYR489 GLN493 SER494 TYR495 GLY496 GLN498 THR500 ASN501 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)
