Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4476 |
| PDBID: | 7NTC |
| Chains: | HL_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.60 |
| Reference: | 10.1126/sciadv.abg7607 |
| Antibody | |
| Antibody: | P008_056 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7NTC_H|Chain D[auth H]|P008_056 Fab Heavy chain|Homo sapiens (9606) MGWSCIILFLVATATGVHSEVQLVESGGGLVKPGGSLRLSCAASGFSFSSYSMNWVRQAPGKGLEWVSSISSNSNYIYYADSMKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCASNRSPYDSSNYYFDYWGQGTRVTISSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSGTKHHHHHH |
Light Chain: L
Mutation: NULL
| >7NTC_L|Chain E[auth L]|P008_056 Fab Light chain|Homo sapiens (9606) MGWSCIILFLVATATGVHCAIRMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQHHDSLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE |
Antigen
Chain: C
Mutation: R713S/R716S/K1017P/V1018P
| >7NTC_C|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MGILPSPGMPALLSLVSLLSVLLMGCVAETGMFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSRASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH |
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)
| Chain residues position delta_SASA
: residuesposition H: GLU20 VAL21 GLY45 PHE46 SER47 TYR51 TYR76 ILE77 TYR78 SER117 ASN118 ARG119 PRO121 TYR122 ASP123 SER124 SER125 ASN126 TYR128 ASP130 TYR131 L: GLN46 ASP47 ILE48 SER49 ASN50 TYR51 TYR68 ASP69 SER71 ASN72 LEU73 GLU74 THR75 GLY76 VAL77 SER79 SER84 GLY85 SER86 HIS110 ASP111 SER112 C: VAL70 SER71 GLY72 GLU96 LYS97 SER98 ASN99 ALA123 THR124 TYR145 HIS146 LYS147 LYS150 SER151 TRP152 MET153 ASP178 LEU179 GLU180 GLY181 LYS182 GLN183 GLY184 ASN185 PHE186 ASN188 LEU212 VAL213 HIS245 ARG246 SER247 TYR248 LEU249 THR259 ALA260 GLY261 ALA262 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
