SMTL ID : 7ydi.1

SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2, focused refinement of RBD region

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.356, H.360, E.384 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.384

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

NAG.2: 4 residues within 4Å: Chain A: K.8, N.72, L.73, T.74 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.73 Hydrogen bonds: A:T.74, A:T.74 NAG.3: 2 residues within 4Å: Chain A: N.35, E.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.35 NAG.4: 2 residues within 4Å: Chain A: N.304, M.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.304 NAG.5: 5 residues within 4Å: Chain A: F.296, S.299, S.402, S.527, N.528 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.402, A:S.527

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, P. et al., SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope. Nat Microbiol (2022)

Release Date

2022-08-24

Peptides

Processed angiotensin-converting enzyme 2: A
Spike protein S1: B
Heavy chain of R1-32: C
Light chain of R1-32: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
H

D
L

Processed angiotensin-converting enzyme 2

Spike protein S1

Heavy chain of R1-32

Light chain of R1-32

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