Complex | |
AACDB_ID: | 5422 |
PDBID: | 7WPD |
Chains: | XY_A |
Organism: | Severe acute respiratory syndrome coronavirus 2, Mus musculus, Lama glama |
Method: | EM |
Resolution (Å): | 3.18 |
Reference: | 10.1126/science.abn8863 |
Antibody | |
Antibody: | JMB2002 Fab |
Antibody mutation: | No |
INN (Clinical Trial): | |
Antigen | |
Antigen: | SARS-CoV-2 Omicron spike glycoprotein |
Antigen mutation: | Yes |
Durg Target: | P0DTC2 |
Antibody
Heavy Chain: X
Mutation: NULL
>7WPD_X|Chain D[auth X]|JMB2002 Fab heavy chain|Mus musculus (10090) QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGRIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCASLASYSSGWEDVFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTHHHHHH |
Light Chain: Y
Mutation: NULL
>7WPD_Y|Chain E[auth Y]|JMB2002 Fab light chian|Mus musculus (10090) GDIQMTQSPSSLSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: A67V/A93I/F140D/206I/G336D/S368L/S370P/S372F/K414N/N437K/G443S/S474N/T475K/E481A/Q490R/G493S/Q495R/N498Y/Y502H/T544K/D611G/H652Y/N676K/P678H/R679S/R680G/R682S/N761K/D793Y/N853K/Q951H/N966K/L978F/K983P/V984P
>7WPD_A|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQ |
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)
X: PHE29 SER30 SER31 ARG50 ILE54 PHE55 GLU74 TYR102 SER103 SER104 GLY105 GLU107 ASP108 Y: SER30 SER31 TRP32 ASP50 TYR91 ASP92 ASN93 LEU94 A: ALA344 THR345 ARG346 ALA348 SER349 TYR351 ALA352 LEU441 LYS444 VAL445 SER446 GLY447 ASN448 TYR449 ASN450 TYR451 LEU452 ILE468 THR470 GLU471 ILE472 GLY482 VAL483 ALA484 CYS488 PHE490 LEU492 |
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)