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Entry information

Complex
AACDB_ID: 6037
PDBID: 8DTK
Chains: CB_A
Organism: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Method: EM
Resolution (Å): 3.77
Reference: 10.1101/2023.12.18.572191
Antibody
Antibody: DH1047 Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: SARS-CoV-2 spike glycoprotein RBD
Antigen mutation: No
Durg Target: P0DTC2

Sequence information

Antibody

Heavy Chain: C
Mutation: NULL

>8DTK_C|Chain C|DH1047 Fab Heavy Chain|Homo sapiens (9606)
QVQLVQSGAEVKKPGASVQVSCQASANTFTNHYIHWVRQAPGQGLEWMGIIYPTGGNTIYAQGFQGRVTMTRDTSLNTIYLELSSLRSEDTAVYYCARDVRVDDSWSGYDLLSGGTYFDYWGQGTLVTVSSAS

Light Chain: B
Mutation: NULL

>8DTK_B|Chain B|DH1047 Fab Light Chain|Homo sapiens (9606)
DIVMTQSPDSLAVSLGERATINCRSSQSVLYSSNNENYLAWYQQKPGQPPKLLIYWASTRESGIPDRFSGSGSGTDFTLTISRLQAEDVAVYYCQQYYSLPRTFGQGTKVEIK

Antigen

Chain: A
Mutation: NULL

>8DTK_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049)
PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTN

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)

B: ASP1 ILE2 SER27 TYR32 TYR91 TYR92 SER93 LEU94 PRO95

C: TRP47 GLY54 GLY55 ASN56 THR57 ILE58 TYR59 ALA60 GLN61 GLN64 ARG71 ASP99

A: TYR369 ASN370 SER371 ALA372 SER373 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 GLY404 ASP405 VAL407 ARG408 GLN409 PRO412 GLY413 GLN414 THR415 GLY416 ASN437 ASN439 PRO499 THR500 ASN501 GLY502 VAL503 GLY504 TYR505 GLN506 TYR508

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)

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