Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5886 |
| PDBID: | 8CIM |
| Chains: | HL_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.00 |
| Reference: | 10.21203/rs.3.rs-2684849/v1 |
| Antibody | |
| Antibody: | BA.2-07 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-COV-2 BA.2.12.1 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >8CIM_H|Chain D, F, H|BA.2-07 FAB HEAVY CHAIN|Homo sapiens (9606) EVQLVQSGAEVKEPGSSVKVSCKASGGSFSTSGISWVRQAPGQGLEWMGVIIPIQGTGNYAQKFQGRVTITADESTTTVYMELSSLRSDDTALYYCARDQHIYDSSGHGGLWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK |
Light Chain: L
Mutation: NULL
| >8CIM_L|Chain E, G, I[auth L]|BA.2-07 FAB LIGHT CHAIN|Homo sapiens (9606) AIRMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKVLIYGASSLHSGVPSRFSGSGSGTDFTLTISRLQPEDFATYYCQQSHSSPRSFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: T19I/L24S/P139D/I210G/C336D/L368F/N370P/A372F/S373A/I402N/D405S/Q414N/N437K/Y449Q/Q474N/A475K/N481A/F490R/Y495R/Q498Y/G502H/L611G/G652Y/T676K/T678H/A701L/T761K/P793Y/V951H/L966K/F1229L
| >8CIM_C|Chain A, B, C|Spike glycoprotein,Fibritin|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGAENLVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK |
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: GLY27 SER28 PHE29 SER30 THR31 TRP47 VAL50 ILE52 ILE54 GLN55 ASN59 TYR60 HIS101 TYR103 SER105 SER106 GLY107 LEU111 L: GLN27 SER30 TYR32 SER91 HIS92 SER93 SER94 ARG96 C: TYR348 TYR446 GLN449 LEU452 PHE453 THR467 GLU468 ILE469 LYS475 PRO476 CYS477 ASN478 GLY479 VAL480 ALA481 GLY482 PHE483 ASN484 CYS485 TYR486 PHE487 LEU489 ARG490 SER491 |
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)
