SMTL ID : 8xsj.1

SARS-CoV-2 Omicron BA.4 RBD + IMCAS-316 + ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: S.420, N.546 No protein-ligand interaction detected (PLIP)

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: N.53, T.55, V.339, Q.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.53 NAG.3: 1 residues within 4Å: Chain A: N.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.90, A:N.90 NAG.4: 3 residues within 4Å: Chain A: Q.81, Q.101, N.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.101 NAG.5: 1 residues within 4Å: Chain A: N.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.322 NAG.6: 2 residues within 4Å: Chain A: F.285, N.432 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.285 NAG.8: 3 residues within 4Å: Chain B: N.25, N.52, F.53 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.52, B:F.53 Hydrogen bonds: B:N.25

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain A: H.374, H.378, E.402 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.374, A:H.378, A:E.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tong, Z. et al., Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1. Cell Rep (2024)

Release Date

2024-07-17

Peptides

Angiotensin-converting enzyme 2: A
Spike protein S1: B
IMCAS-316 H chain: C
IMCAS-316 L chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Angiotensin-converting enzyme 2

Spike protein S1

IMCAS-316 H chain

IMCAS-316 L chain

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