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Entry information

Complex
AACDB_ID: 6560
PDBID: 7SI0
Chains: CD_A
Organism: Homo sapiens
Method: XRD
Resolution (Å): 3.00
Reference: 10.1038/s41467-021-27397-z
Antibody
Antibody: Omalizumab variant 813 Fv
Antibody mutation: Yes
INN (Clinical Trial):
Antigen
Antigen: IgE Fc
Antigen mutation: No
Durg Target: P01854

Sequence information

Antibody

Heavy Chain: C
Mutation: G16D/I53V

>7SI0_C|Chain B[auth C], D[auth E], I, K|813 Variable fragment Heavy chain|Homo sapiens (9606)
SEVQLVESGGGLVQPDGSLRLSCAVSGYSITSGYSWNWIRQAPGKGLEWVASVTYDGSTNYNPSVKGRITISRDDSKNTFYLQMNSLRAEDTAVYYCARGSHYFGHWHFAVWGQGTLVTVSSG

Light Chain: D
Mutation: Y33S

>7SI0_D|Chain C[auth D], E[auth F], J, L|813 Variable fragment Light chain|Homo sapiens (9606)
GSDIQLTQSPSSLSASVGDRVTITCRASQSVDSDGDSYMNWYQQKPGKAPKLLIYAASYLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSHEDPYTFGQGTKVEIKGGSENLYFQGGSGHHHHHHHH

Antigen

Chain: A
Mutation: NULL

>7SI0_A|Chain A, F[auth B], G, H|IgE Fc|Homo sapiens (9606)
APMAEGGGQNHHHHHHHHGGENLYFQGGSCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP

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)

C: TYR27 SER31 GLY32 TYR33 TYR54 SER100 HIS101 TYR102 PHE103 TRP106

D: ASP30 ASP32 GLY33 ASP34 SER35 TYR36 TYR53 ALA55 TYR57 GLY70 SER71

A: THR373 TRP374 SER375 ARG376 ALA377 SER378 GLY379 LYS380 PRO381 GLU412 GLY413 GLU414 GLN417 ARG419 THR421 ARG427 ALA428 MET430

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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