Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3773 |
| PDBID: | 7FJN |
| Chains: | IJ_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.25 |
| Reference: | 10.1016/j.isci.2022.104043 |
| Antibody | |
| Antibody: | T6 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 B.1.351 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7FJN_I|Chain D[auth H], E[auth I]|T6 heavy chain|Homo sapiens (9606) QVQLQQPGTELVNPGASLKMSCKTSGYRFTSYIIHWVKQTPGQGLEWIGAIFPENDDTSYSQKFKGKATLTTDTSSSTAYMQLSSLTSEDSAVYYCARDGENVLDYWGQGTSVTVSS |
Light Chain: J
Mutation: NULL
| >7FJN_J|Chain F[auth J], G[auth L]|T6 light chain|Homo sapiens (9606) QIVLTQSPSSLAVSVGEKVTLSCKSSQSLLYSNNQKNYLAWYQQKSGRSPKLLLHWTSTRESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYTYPWTFGGGTKLEIK |
Antigen
Chain: A
Mutation: L3F/D65A/D200G/T287T/Q399N/N466K/Q483V/L596G/N664G/S665S/R667S/S683V/R968P/L969P
| >7FJN_A|Chain A, B, C|Spike glycoprotein,Envelope glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) VNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKTFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGVENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEKGSDYKDDDDK |
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)
| I: TYR32 ILE33 TRP47 PHE52 GLU54 ASN55 ASP56 ASP57 THR58 SER59 TYR60 LYS65 ASP99 GLY100 GLU101 J: TYR31 SER32 ASN33 TYR38 TRP56 TYR97 TYR98 THR99 TYR100 PRO101 TRP102 A: ASN417 TYR421 LEU455 PHE456 ARG457 LYS458 TYR473 GLN474 ALA475 GLY476 SER477 THR478 PRO479 ASN481 PHE486 ASN487 TYR489 GLN493 |
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)
