Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5928 |
| PDBID: | 8CYC |
| Chains: | E_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Lama glama |
| Method: | EM |
| Resolution (Å): | 2.90 |
| Reference: | 10.1016/j.celrep.2022.111004 |
| Antibody | |
| Antibody: | 2-34 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: E
Mutation: NULL
| >8CYC_E|Chain D, E, F|pan-sarbecovirus nanobody 2-34|Lama glama (9844) HVQLVESGGGLVQAGGSLRLSCAASGRTFSRYAAGWFRQAPGKEREFVAVIEWDGDSAYYADPVKGRFTISRDNAKNTVYLQMNRLKPEDTAVYICAVGGNHYSRSKYYNLDEYDDWGQGTQVTVSS |
Antigen
Chain: B
Mutation: NULL
| >8CYC_B|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT |
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)
| E: HIS1 VAL2 ARG27 THR28 ARG31 TYR32 GLU52 TRP53 ASP54 ASP56 GLY100 ASN101 HIS102 TYR103 LYS107 ASP112 GLU113 TYR114 ASP115 ASP116 TRP117 B: TYR369 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 LYS386 ASP405 VAL407 ARG408 ALA411 PRO412 GLY413 GLN414 THR415 PRO426 ASP427 ASP428 PHE429 THR430 |
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)
