Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5497 |
| PDBID: | 7WWL |
| Chains: | JN_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.00 |
| Reference: | 10.1038/s41392-022-00987-z |
| Antibody | |
| Antibody: | ZWD12 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Delta spike glycoprotein ECD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: J
Mutation: NULL
| >7WWL_J|Chain D[auth H], F[auth I], H[auth J]|heavy chain of ZWD12|Homo sapiens (9606) EVQLVESGGGLVQPGGTLRLSCVASGFSFSNYWMSWVRQAPGKGLEWVANIKQDGSETHYVDSVKGRFTISRDNAKNSLYLQMNSLRADDTAVYFCVKDRTDWELIRGYFGHWGQGTQITVSS |
Light Chain: N
Mutation: NULL
| >7WWL_N|Chain E[auth L], G[auth M], I[auth N]|light chain of ZWD12|Homo sapiens (9606) DIVMTQTPSSLSLSPGDRATLSCRASENIINYLAWYQQRPGQSPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRIIWPPYTFGQGTKVDIK |
Antigen
Chain: A
Mutation: T19R/G142D/E156G/N450R/G476K/Y612G/B679R/R815P/A890P/P897P/S940P/L948N/L984P/D985P
| >7WWL_A|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSRRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQNVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT |
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)
| J: GLU57 HIS59 LYS65 TRP103 GLU104 LEU105 ILE106 ARG107 N: ASP1 GLU27 ASN28 ILE29 ILE30 TYR32 ASP50 ASN53 ARG91 ILE92 ILE93 TRP94 PRO95 TYR97 A: PHE342 ASN343 ALA372 SER373 SER375 TRP436 ASN437 SER438 ASN439 ASN440 LEU441 SER443 LYS444 VAL445 PRO499 THR500 ASN501 GLY502 VAL503 GLN506 TYR508 ARG509 |
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)
